Software/list

Below is (one of many possible) dynamic tables of software data, created from pages in the wiki. To add a package to the list, use the following form:

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Name	Summary	Bio Tags	Meth Tags	Features	Language	Licence	OS
4peaks	Allows viewing sequencing trace files, motif searching trimming, BLAST and exporting sequences.	Sequencing	Sequence analysis			Freeware	Mac OS X
AB Large Indel Tool	Identifies deviations in clone insert size that indicate intra-chromosomal structural variations compared to a reference genome.	InDel discovery Sequencing	Mapping		Perl	GPL	Linux 64
AB Small Indel Tool	The SOLiD™ Small Indel Tool processes the indel evidences found in the pairing step of the SOLiD™ System Analysis Pipeline Tool (Corona Lite).	InDel discovery Sequencing	Mapping Alignment		Perl C++	GPL	Linux 64
ABBA	Assembly Boosted By Amino acid sequence is a comparative gene assembler, which uses amino acid sequences from predicted proteins to help build a better assembly	Genomic Assembly	Assembly Scaffolding			Artistic License	Linux
ABMapper	Maps RNA-Seq reads to target genome considering possible multiple mapping locations and splice junctions	Genomics Transcriptomics	Mapping Alignment		C++ Perl	GPLv3	Linux
ABySS	ABySS is a de novo sequence assembler designed for short reads and large genomes.	De-novo assembly	Assembly De Bruijn graph	MPI OpenMP	C++	Commercial Freeware	POSIX Linux Mac OS X
Adapter Removal (software)	Removes adaptor fragments from raw short read sequence data and outputs data to FASTA format.	General bioinformatics (pipeline)	Adapter Removal (software)	Trimming	Java	Custom Licence	Linux 64 Windows Mac OS X
AGE	AGE is a tool that implements an algorithm for optimal alignment of sequences with SVs.	Structural variation	Alignment Gap extension			Creative Commons license (Attribution-NonCommerical).
AGILE	A hash table based high throughput sequence mapping algorithm for longer 4A54 reads that uses diagonal multiple seed-match criteria, customized q-gram filtering and a dynamic incremental search approach among other heuristics to optimize every step of the mapping process		Mapping		C
Agp2amos	missing		Format conversion				Windows Linux
Alcovna	ALgorithms for COmparing and Visualizing Non Assembled data	SNP discovery			Java
ALEXA-Seq	Alternative Expression Analysis by massively parallel RNA sequencing	RNA-Seq Quantitation Alternative Splicing			Perl	GPLv3
ALLPATHS	De novo assembly of whole-genome shotgun microreads.	De-novo assembly	Assembly De Bruijn graph
Alta-Cyclic	Alta-Cyclic is a Illumina Genome-Analyzer (Solexa) base caller.		Basecaller
AMOS	AMOS is a Modular, Open-Source whole genome assembler.		Assembly Assembly validation Assembly visualization Format conversion Integrated Solution		C Perl		Linux
ANCHOR	Post-processing tools for de novo assemblies		Assembly Assembly QC		C++ Python	BCCA (academic use)	Linux
Anno-J	Annotation Browsing 2.0		Visualization			Creative Commons - Attribution-NonCommercial-ShareAlike
ANNOVAR	ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data	Genomics Genetics	Annotation Variant Prioritization	Gene-based annotation region-based annotation filter-based annotation	Perl	Commercial Freeware	Linux Windows Mac OS X
Arachne	ARACHNE is a program for assembling data from whole genome shotgun sequencing experiments.		Assembly OLC
AREM	AREM: Aligning Short Reads from ChIP-Sequencing by Expectation Maximization	ChIP-Seq	Peak calling Mapping		Python		Linux
Arf	arf is a genetic analysis program for sequencing data.
Array Suite (Array Studio/Server)	Array Studio is a complete analysis and visualization package for NextGen sequencing data, as well as other -OMIC data types. Array Server is a backend enterprise server for storage and analysis of -OMIC and NextGen sequencing data.	Genomics SNP discovery InDel discovery	Mapping Expression profiling	Data Visualisation Variant annotation and analysis coverage analysis Mapping	C#	Commercial	Windows
ArrayExpressHTS	R-based pipeline for RNA-Seq data analysis.	RNA-Seq RNA-Seq Quantitation			R
ArrayStar	ArrayStar is an easy-to-use gene expression analysis software package that offers powerful visualization and statistical tools to help you analyze your microarray data.	Gene Expression Analysis	Differentially expressed gene identification Gene ontology analysis Sequence variation analysis Statistics			Commercial	Windows Mac OS X 10.6 with Parallels Desktop
ASC	Empirical Bayes method to detect differential expression.	RNA-Seq Quantitation	Empirical Bayes
ATAC	ATAC is a computational process for comparative mapping between two genome assemblies, or between two different genomes.		Assembly validation Alignment				Linux
Atlas Suite	Atlas is a suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in Whole Exome Capture Sequecing (WECS) data. SNPs may be called using the Atlas-SNP2 application and indels may be called using the Atlas-Indel2 application.	SNP discovery InDel discovery	Variant Calling		Ruby C	BSD	POSIX
Atlas-SNP2	Atlas-SNP2 is a SNP discovery tool developed for next generation sequencing platforms	SNP discovery			Ruby	Freeware	UNIX
Avadis NGS	Avadis NGS is a desktop software platform for alignment, analysis, visualization, and management of data generated by next-generation sequencing (NGS) platforms. It supports workflows for RNA-Seq, DNA-Seq, and ChIP-Seq analysis and is designed with the biologist in mind.	ChIP-Seq DNA-Seq RNA-Seq Small RNA Pathway analysis	Alignment Quality Control Sequence analysis Visualization Biological Contextualization	Rich Visualization Identify effects of SNPs on transcripts Identify Structural Variants from Paired Reads (Insertions Deletions Translocations Inversions) Identify binding site peaks in ChIP-Seq data Identify motifs around binding sites Determine gene expression levels and identify differentially expressed genes De-convolve transcript expression levels and identify differential splice variants Identify Novel Exons Identify Novel Splice Junctions Identify Fusion Genes Perform QC on Reads determine on-and off-target reads and filter anomalous reads Determine Enriched GO Terms Determine Significant Pathways	Java R	Commercial	Windows Linux Mac OS X
Baa.pl	use transcripts to assess a de novo assembly	Genomic Assembly Evaluation Genomic Assembly Validation	Alignment Analysis		Perl	GPL	any
Bambino	Variant detector and graphical alignment viewer for SAM/BAM format data.	SNP discovery Somatic mutations			Java
Bambus	Bambus is a general purpose scaffolder		Scaffolding
BAMseek	BAMseek is a large file viewer for BAM and SAM alignment files.	Genomics Transcriptomics	Alignment viewer		Java	GPLv3	Cross-Platform
BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.		Programming Library Alignment Analysis		C++	MIT	Cross-Platform
BamView	Interactive Java application for visualising the large amounts of data stored for sequence reads which are aligned against a reference genome sequence		Visualization		Java	GPL	Mac OS X UNIX Windows
Barcode generator	Generator of sequence barcodes suitable for Illumina sequencing.		Sample Barcoding		Python
Barcrawl Bartab	Barcrawl facilitates the design of barcoded primers, for multiplexed high-throughput sequencing.		Sample Barcoding			GPL
BarraCUDA	Barracuda is a high-speed sequence aligner based on BWA and utilizes the latest Nvidia CUDA architecture for accelerating alignments of sequence reads generated by the next-generation sequencers.	Sequence analysis	Mapping Alignment FM-Index GPU	Gapped and ungapped alignment paired-end mapping GPGPU parallel execution	C C++ CUDA	GPLv3 MIT	Linux
Batman	Bayesian tool for methylation analysis (Batman) €”for analyzing methylated DNA immunoprecipitation (MeDIP) profiles	DNA methylation			Java	LGPL
BayesCall	Bayesian basecaller	Sequencing	Basecaller		C++ Python	GPLv3
BayesPeak	A Bayesian hidden Markov model to detect enriched locations in ChIP-seq data.	ChIP-Seq	Hidden Markov Model MCMC	Multicore	R	GPL
BaySeq	Identify differential expressed genes	RNA-Seq Quantitation	Differentially expressed gene identification		R
BBSeq	Tool for analyzing RNA-Seq data to analyze gene expression	RNA-Seq Quantitation			R
Bcbio-nextgen	Python scripts and modules for automated next gen sequencing analysis. These provide a fully automated pipeline for taking sequencing results from an Illumina sequencer, converting them to standard Fastq format, aligning to a reference genome, doing SNP calling, and producing a summary PDF of results.	General bioinformatics (pipeline)	QC Filtering Trimming Mapping Peak calling Motif detection Differential expression Genomic region matching Aligning Genotyping		Python	MIT	platform-independent
BEADS	ChIP-Seq data normalization for Illumina	ChIP-Seq	Normalization
BEAP	The Blast Extension and Assembly Program (BEAP) uses a short starting DNA fragment to recursively blast nucleotide databases to obtain all sequences that overlaps to construct the a "full length" sequence.		Mapping
BEDTools	BEDTools is an extensive suite of utilities for comparing genomic features in BED format.	Genomics	Mapping	Feature overlaps UNIX pipes coverage split-alignments BAM support	C++	GPLv2	Linux Mac OS X
Bedutils	NGSUtils is a suite of software tools for working with next-generation sequencing datasets. Staring in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working with next-generation sequencing data. We initially started doing custom coding for each project in a one-off manner. It quickly became apparent that this was an inefficient manner to work, so we started assembling smaller utilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia, SOLiD and 454 sequencing data. We have used them for DNA and RNA resequcing, ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting). These tools are also used heavily in our in-house DNA and RNA mapping pipelines. These tools have of great use within our lab group, and so we are happy to make them available to the greater community. NGSUtils is made up of 50+ programs, mainly written in Python. These are separated into modules based on the type of file that is to be analyzed. There are four modules:
Belvu	An X-windows viewer for multiple sequence alignments		Multiple sequence alignment viewer				Linux
BFAST	Blat-like Fast Accurate Search Tool.	Whole Genome Resequencing	Mapping Alignment Genome Indexing Colorspace	parallel execution command line	C	GPL	Solaris UNIX
BFCounter	BFCounter is a program for counting k-mers in DNA sequence data.		K-mer analysis		C++
BING	biomedical informatics pipeline (BING) for the analysis of NGS data that offers several novel computational approaches to 1. image alignment, 2. signal correlation, compensation, separation, and pixel-based cluster registration, 3. signal measurement and base calling, 4. quality control and accuracy measurement.		Basecaller Sequencing Quality Control
Bionimbus	Cloud environment for analysis of microarray and second generation sequencing data.						Linux Amazon EC2 cloud
Biopieces	The Biopieces are a collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. The Biopieces work on a data stream in such a way that the data stream can be passed through several different Biopieces, each performing one specific task: modifying or adding records to the data stream, creating plots, or uploading data to databases and web services.	Genomics	Alignment Quality Control Sequence analysis Visualization		Perl Python Ruby C	GPLv2
Biopython	Biopython provides a tool kit for writing bioinformatics and computational molecular biology software in Python.	Sequence analysis Phylogenetics Population genetics Protein structures	Sequence parsing Command line tool wrappers Programming Library	Various	Python	Biopython License (MIT/BSD style)	Linux Windows Mac OS X
BioSmalltalk	BioSmalltalk provides an environment to build bioinformatics scripts and applications using the most powerful object technology as of today, the Smalltalk programming environment	Sequence analysis Phylogenetics Population genetics Protein structures	Sequence parsing Command line tool wrappers Programming Library	Various	Smalltalk		Linux Windows Mac OS X
BiQ Analyzer	BiQ Analyzer is a software tool for easy visualization and quality control of DNA methylation data. With more than 2,000 downloads so far, BiQ Analyzer has become a standard tool for processing DNA methylation data from bisulfite sequencing.	Epigenomics DNA methylation			Java		Windows Linux Mac OS X Solaris
BiQ Analyzer HT	BiQ Analyzer HT is an enhanced version of BiQ Analyzer that provides extensive support for high-throughput bisulfite sequencing. BiQ Analyzer HT facilitates the processing, quality control and initial analysis of single-basepair resolution DNA methylation data. It was developed for deep bisulfite sequencing of one or more loci using the Roche 454 platform, but it easily extends to other sequencing platforms. BiQ Analyzer HT features a biologist-friendly graphical user interface, a fast alignment algorithm and a variety of ways to visualize DNA methylation data.	Epigenomics DNA methylation Bisulfite Sequencing			Java		Windows Linux Mac OS X Solaris
Bis-SNP	BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq and RRBS) on Illumina platform. It uses bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously.	SNP discovery Genotyping DNA methylation Bisulfite Sequencing	Bisulfite SNP calling Methylation Calling MapReduce	Accurate SNP and methylation calling in Bisulfite-seq/NOMe-seq/RRBS	Java Perl	MIT	Linux Mac OS X
Bismark	Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.	Epigenomics Genomics DNA methylation	Bisulfite mapping Mapping Methylation Calling	fast and convenient Bisulfite-Seq output very flexible	Perl	GPLv3	Linux Mac OS X Windows
BLAST	...it's BLAST.						Linux
BLAT	Fast, accurate spliced alignment of DNA sequences		Mapping Alignment	Mapping	C	Freeware	Linux Mac OS X
Blixem	a graphical blast viewer	Sequence analysis Phylogenetics Homology	Alignment viewer Multiple sequence alignment viewer			GPL	Linux
BOAT	Can accurately and efficiently map sequencing reads back to the reference genome.		Mapping			GPL
Bort	Bort parses Blast output and quantifies hits by contig and read counts.	RNA-Seq Quantitation			Perl		any
Bowtie	Bowtie is an ultrafast, memory-efficient short read aligner.		Mapping Burrows-Wheeler FM-Index				Mac OS X Linux Windows
BRAT	accurate and efficient tool for mapping short reads obtained from the Illumina Genome Analyzer following sodium bisulfite conversion. Both single and paired ends are supported.	Epigenomics DNA methylation	Bisulfite mapping Mapping			GPLv3
BRCA-diagnostic	Computational screening test for BRCA1/2 mutants in human genomic DNA	Personal genomics			Perl
BreakDancer	BreakDancer is an application for detecting structural rearrangements and indels in short read sequencing data	Genomics Structural variation InDel discovery			Perl C++	GPLv3
Breakpointer	Breakpointer is a fast tool for locating sequence breakpoints from the alignment of single end reads (SE) produced by next generation sequencing (NGS). It adopts a heuristic method in searching for local mapping signatures created by insertion/deletions (indels) or more complex structural variants(SVs). With current NGS single-end sequencing data, the output regions by Breakpoint mainly contain the approximate breakpoints of indels and a limited number of large SVs.	Exome and Whole genome variant detection InDel discovery	Statistical testing		C++ Perl	GPL
BreakSeq	Database of known human breakpoint junctions and software to search short reads against them.	Structural variation	Mapping
Breakway	Breakway is a suite of programs that take aligned genomic data and report structural variation breakpoints.	Whole Genome Resequencing Genomics Structural variation InDel discovery	Sequence analysis Genetic variation annotation	Fast specific UNIX pipes	Perl	GPL	Linux Mac OS X Windows
BS Seeker	Mapping tool for bisulfite treated reads	Epigenomics	Bisulfite mapping		Python
BS-Seq	The source code and data for the "Shotgun Bisulphite Sequencing of the Arabidopsis Genome Reveals DNA Methylation Patterning" Nature paper by Cokus et al. (Steve Jacobsen's lab at UCLA). POSIX.	Epigenomics	Bisulfite mapping
BSMAP	short reads mapping software for bisulfite sequencing	DNA methylation	Mapping Bisulfite mapping	Bisulfite sequencing	C++	GPLv3	Linux 64
BSSim	BSSim: Bisulfite sequencing simulator for next-generation sequencing.	DNA methylation Bisulfite Sequencing	Simulation	BSSim can allow users to mimic various methylation level.	Python	GPL v3	UNIX Linux Mac OS X Windows
Btrim	Btrim is a fast and lightweight software to trim adapters and low quality regions in reads.		Trimming				Linux
BWA	Fast, accurate, memory-efficient aligner for short and long sequencing reads	Mapping Read alignment	FM-Index	Gapped alignment paired-end mapping	C	GPLv3 MIT	UNIX
BWA-SW	Fast, accurate, memory-efficient aligner for long sequencing reads	Mapping Read alignment	FM-Index	Gapped alignment Local alignment	C	GPLv3 MIT	UNIX
CABOG	Celera Assembler is scientific software for DNA research.	De-novo assembly	Assembly	Robust to homopolymer run length			Linux
CANGS	CANGS is a flexible and user-friendly utility to trim sequences, filter low quality sequences, and produce input files for further downstream analyses for 454 sequences. CANGS can be used to assign the taxonomic grouping based on similarity with sequences from the NCBI database	Metagenomics Phylogenetics	Primer removal Trimming Sequencing Quality Control
CARPET	A web‐based package for the analysis of ChIP‐chip and expression tiling data	ChIP-on-chip	Tilling		C++
CASHX	Parse, map, quantify and manage large quantities of short-read sequence data.	Small RNA transcriptome	Mapping
CATCH	A tool for exploring patterns in ChIP profiling data.	ChIP-Seq ChIP-on-chip	Clustering and alignment	parallel execution graphical browsing of results	Java	Open Source
CatchAll	Estimate ecological diversity with both parametric and non-parametric estimators.	Population genetics Metagenomics
CGA Tools	Tools for viewing, manipulating and converting data from Complete Genomics		Conversion		C++	Apache License 2.0	Linux UNIX Mac OS X
ChimeraScan	Identifies chimaeric transcripts in RNA-Seq data	Fusion transcripts
ChIP-Seq (application)	The ChIP-Seq web server provides access to a set of useful tools performing common ChIP-Seq data analysis tasks, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. It is an open system designed to allow interoperability with other resources, in particular the motif discovery programs from the Signal Search Analysis (SSA) server.	ChIP-Seq Analysis	Read Mapping and Tag Distribution Analysis		C Perl	GPL	Linux Mac OS X
ChIPmeta	Combining data from ChIP-seq and ChIP-chip.	Transcription Factor Binding Site identification ChIP-Seq ChIP-on-chip	Hidden Markov Model
ChIPMunk	ChIPMunk is a fast heuristic DNA motif digger based a on greedy approach accompanied by bootstrapping. ChIPMunk identifies the strong motif with the maximum Kullback Discrete Information Content in a given set of DNA sequences. *NEW URL* http://autosome.ru/ChIPMunk	ChIP-Seq Motif analysis Motif discovery	Motif analysis Motif discovery	efficient motif discovery for huge datasets up to tens of thousands of sequences; multi-core CPU support; usage of the ChIP-Seq base coverage peak data	Java	Freeware	platform-independent
CHiPSeq	From Science Johnson, 2007	ChIP-Seq	Peak calling
ChIPseqR	ChIP-seq qanalysis tool	ChIP-Seq			R
Chipster	User-friendly NGS data analysis software with built-in genome browser and workflow functionality. Chipster includes tools for ChIP-seq, RNA-seq, miRNA-seq and MeDIP-seq analysis, and functionality for exome-seq and CGH-seq will soon be added.	ChIP-Seq RNA-Seq MiRNA-Seq MeDIP-Seq	QC Filtering Trimming Mapping Peak calling Motif detection Differential expression Pathway analysis Methylation analysis Genomic region matching Genome browser		Java R	GPLv3	platform-independent
ChromaSig	An unsupervised learning method, which finds, in an unbiased fashion, commonly occurring chromatin signatures in both tiling microarray and sequencing data.	ChIP-on-chip	Chromatin motif finding		Perl C
ChromHMM	ChromHMM is software for learning and characterizing chromatin states.	Epigenomics	Hidden Markov Model Segmentation		Java	GPL 2
CisGenome	An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis	ChIP-Seq ChIP-on-chip Motif analysis Gene annotation retrieval	Gibbs motif sample		C C++		UNIX Windows
Cistrome	Galaxy-based web service for analysis of ChIP data	ChIP-on-chip ChIP-Seq			Python
CLCbio Genomics Workbench	De novo and reference assembly SNP and small indel detection and annotation.	Genomics Whole Genome Resequencing De-novo assembly SNP discovery InDel discovery ChIP-Seq RNA-Seq Alignment RNA-Seq MiRNA Alignment Transcriptomics	Mapping Assembly Alignment Colorspace BLAST Ab-inito gene prediction Adapter Removal (software) Annotation Assembly QC Basespace Bisulfite SNP calling De Bruijn graph Heatmaps	Advanced and user-friendly analyses of genomic transcriptomic and epigenomic NGS data in a graphical user-interface. Wizard driven tools and a freely available developer toolkit SIMD implementation multi-threading hybrid assembly Integrated solution	Java C++	Commercial	Windows Mac OS X Linux
Clean reads	clean_reads cleans NGS (Sanger, 454, Illumina and solid) reads.		Trimming Sequencing Quality Control		Python
CleaveLand	A pipeline for using degradome data to find cleaved small RNA targets.	MiRNA			Perl R	Freeware
CLEVER	CLEVER is a tool to discover structural variations such as (larger) insertions and deletions in genomes from paired-end sequencing reads.	Genomics Structural variation Copy number estimation	Structural variation discovery	command line	C++ Python	GPLv3	any
ClipCrop	a new method and implementation named ClipCrop for detecting SVs with single-base resolution
CloudAligner	Hadoop-based short read aligner		Mapping Hadoop		Java	GPL	cloud
CloudBurst	CloudBurst is a parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes.	SNP discovery Genotyping Personal genomics	Mapping MapReduce Hadoop	parallel execution Hadoop Academic Cloud Computing Initiative	Java
ClustDB	A powerful tool for exact sequence matching						Linux
CNANorm	A normalization method for Copy Number Aberration in cancer samples.	Cancer biology Copy number estimation Genomics	Mixture model Peak detection Normalization		R Perl	GPLv2	Linux Mac OS X Windows
CNAseg	We present a novel approach, called CNAseg, to identify CNAs from second-generation sequencing data. It uses depth of coverage to estimate copy number states and flowcell-to-flowcell variability in cancer and normal samples to control the false positive rate.	Structural variation
CNAseg	We present a novel approach, called CNAseg, to identify CNAs from second-generation sequencing data. It uses depth of coverage to estimate copy number states and flowcell-to-flowcell variability in cancer and normal samples to control the false positive rate.	Structural variation
CNB MetaGenomics tools	A number of tools and meta-tools developed at CNB/CSIC for the analysis of metagenomics data (some rely on QIIME).	Metagenomics Biodiversity Community analysis High-throughput sequencing	Community Analysis		Bash Perl Python C	EU-GPL	Linux Unix-like POSIX
CnD	Program to detect copy number variation in inbred mouse strains	Copy number estimation	Hidden Markov Model		D	GPL
CNVer	CNVer is a method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation. CNVer combines this information within a unified computational framework called the donor graph, allowing it to better mitigate the sequencing biases that cause uneven local coverage. CNVer can also reconstruct the absolute copy counts of segments of the donor genome, and work with low coverage datasets.	Structural variation Copy number estimation			Perl C++
CnvHMM	WashU copy number variant (CNV) detection algorithm for Illumina/Solexa data.	Structural variation					Linux
CNVnator	CNV discovery and genotyping from read-depth analysis of personal genome sequencing	Copy number estimation Genotyping
CNVseq		Copy number estimation			Perl R
CompreheNGSive	compreheNGSive is an interactive visualization of the end results of the next-generation sequencing pipeline.	Next Generation Sequencing	Visualization		Python Qt	LGPL	Mac OS X Linux
CoNAn-SNV	CoNAn-SNV is a probabilistic framework for the discovery of single nucleotide variants in WGSS data. This software explicitly integrates information about copy number state of different genomic segments into the inference of single nucleotide variants.	SNP discovery			C
ConDeTri	ConDeTri is a content dependent read trimming software for Illumina/Solexa sequencing data	RNA-Seq DNA-Seq Genomics	Trimming		Perl
ContEst	GATK tool to estimate amount of cross-individual contaminating sequence in a dataset		Sequencing Quality Control		Java	BSD
Contra	Copy number analysis for exome-sequencing / targeted-resequencing. Two methods of analysis available: Case vs Control, or Case vs Baseline. Function available for creating a baseline from multiple samples.	Next Generation Sequencing Cancer biology Genomics Copy number estimation		Copy number analysis baseline (pseudo-control) creation	Python R	GPL v3	Linux 64 Linux
Contrail	A Hadoop based genome assembler for assembling large genomes in the clouds	De-novo assembly	Assembly De Bruijn graph Hadoop
CopySeq	CopySeq analyzes the depth-of-coverage of whole genome resequencing data to predict CNVs and to infer quantitative locus copy-number genotypes.	Structural variation Copy number estimation Genotyping Personal genomics			Java R		Mac OS X Linux
Coral	Corrects sequencing errors in short read data via multiple alignments		Error correction		C++
CORAL (Contig Ordering Algorithm)	An algorithm has been developed to order fingerprinted clones within contigs.		Error correction		Java
Cortex	Cortex is an efficient and low-memory software framework for analysis of genomes using sequence data. Cortex allows de novo assembly of variants without having to do a consensus assembly first. Also allows comparison of genomes without using consensus, and alignment of sequence data to a de Bruijn graph	Genomics	Assembly Variant Calling		C	GPLv3
CPTRA	Integrated transcriptome analysis from Sanger, 454, Solexa, SOLiD, etc reads	RNA-Seq Alignment RNA-Seq Quantitation			Python
CPTRA	Integrated transcriptome analysis from Sanger, 454, Solexa, SOLiD, etc reads	RNA-Seq Alignment RNA-Seq Quantitation			Python
CRAC	CRAC is a mapping software specialized for RNA-Seq data. It detects mutations, indels, splice or fusion junctions in each single read.	Mapping RNA Seq analysis RNA-Seq Alignment Alternative Splicing Fusion genes Fusion transcripts SNP discovery InDel discovery	Mapping Read mapping Burrows-Wheeler FM-Index		C++	CeCILL	Linux Linux 64 Mac OS X
CRISP	Identifies rare and common variants in pooled sequencing data	SNP discovery	Pooled samples		Python
Crossbow	Crossbow is a cloud-computing software tool that combines the aligner BOWTIE and the SNP caller SOAPsnp.	SNP discovery	Mapping MapReduce Hadoop
Crossbow	Crossbow is a cloud-computing software tool that combines the aligner BOWTIE and the SNP caller SOAPsnp.	SNP discovery	Mapping MapReduce Hadoop
CUDA-EC	A scalable parallel algorithm for correcting sequencing errors in high-throughput short-read data so that error-free reads can be available before DNA fragment assembly.		Sequencing Quality Control GPU	read error correction	C
Cufflinks	Cufflinks assembles transcripts and estimates their abundances in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.	RNA-Seq Alignment RNA-Seq Quantitation Differential Expression Alternative Splicing De novo transcriptome assembly RNA-Seq	Assembly Differentially expressed gene identification Statistical testing			Boost
CummeRbund	Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.	RNA-Seq Quantitation	Visualization
Curtain	Curtain is a Java wrapper around next-generation assemblers such as Velvet which allows the incremental introduction of read-pair information into the assembly process. This enables the assembly of larger genomes than would otherwise be possible within existing memory constraints.	De-novo assembly	Assembly De Bruijn graph			Apache License 2.0
Cutadapt	remove adapter sequences from high-throughput sequencing data using alignment				Python C	MIT
DecGPU	Parallel and distributed error correction algorithm for high-throughput short reads.	De-novo assembly	Error correction GPU		C++	GPLv3	Linux
DeconSeq	DeconSeq can be used to automatically detect and efficiently remove any type of sequence contamination from metagenomic datasets, including human or other host sequences. The tool uses a modified version of the BWA-SW aligner and can be applied to longer-read datasets (150+bp read length). DeconSeq is available as both standalone and web-based versions.	Metagenomics Metatranscriptomics Genomics	Contaminant filtering		Perl C	GPLv3	UNIX Mac OS X
DeFuse	deFuse is a software package for gene fusion discovery using RNA-Seq data. The software uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. The software also employs a number of heuristic filters in an attempt to reduce the number of false positives and produces a fully annotated output for each predicted fusion	Fusion genes RNA-Seq Fusion transcripts
DEGseq	an R package to identify differentially expressed genes or isoforms for RNA-seq data from different samples	RNA-Seq Quantitation	Differentially expressed gene identification		R
DESeq	DESeq is an R package to analyse count data from high-throughput sequencing assays such as RNA-Seq and test for differential expression.	RNA-Seq Quantitation ChIP-Seq	Statistical testing Sequencing Quality Control		R	GPLv3	UNIX Windows Mac OS X
DIAL	A computational pipeline for identifying single-base substitutions between two closely related genomes without the help of a reference genome.	SNP discovery Comparative genomics			C Python	MIT	Linux
DiBayes	Bayesian identification of SNPs in color space (SOLiD) data	SNP discovery	Colorspace			GPL
Diffreps	diffReps is developed to find different peaks in ChIP-seq. It scans the whole genome using a sliding window, performing millions of statistical tests and report the significant hits. diffReps takes into account the biological variations within a group of samples and uses that information to enhance the statistical power. Considering biological variation is of high importance, especiallly for in vivo brain tissues.	Epigenomics	ChIP seq	Multiple sample information used.	Perl	GPLv3	Linux Windows Mac OS X
Dindel	Calls small indels from short-read sequence data	InDel discovery	Localized reassembly/realignment
DNA Baser	Tool for manual and automatic sequence assembly, analysis, editing, sample processing, metadata integration, file format conversion and mutation detection.	Structural variation SNP discovery	Assembly Assembly editing Sequence analysis	Portable. Does not require installation. Can run from USB stick. Only 3MB.	Compiled	Commercial Freeware	Windows
DNA Chromatogram Explorer	DNA Chromatogram Explorer is a Windows Explorer clone dedicated to DNA sequence analysis and manipulation.		Chromatogram management Chromatogram viewer Conversion	Portable. Does not require installation. Can run from USB stick. Only 1MB.		Freeware	Windows
DNAA	DNAA (DNA Analysis) software for analysis of Next-Generation Sequencing data.	Structural variation SNP discovery DNA methylation	Statistics Sequencing Quality Control Simulation			GPL
DNAzip	A series of techniques that in combination reduces a single genome to a size small enough to be sent as an email attachment.		Data compression		C++
DrFAST	Fast mapper for dibase encoded data.
DSAP	Automated multiple-task web service designed to provide a total solution to analyzing deep-sequencing small RNA datasets generated by next-generation sequencing technology	Small RNA transcriptome MiRNA					browser based
DSGseq	This program aims to identify differentially spliced genes from two groups of RNA-seq samples.	RNA-Seq Differential Expression Alternative Splicing	RNA-Seq analysis Differential expression Alternative Splicing Statistical testing		C R	Commercial Freeware	Linux Windows Mac OS X
DSRC	Compression algorithm for genomic data in FASTQ format		Data compression
E-miR	Perl tools for processing miRNA sequencing data	Small RNA transcriptome MiRNA
Ea-utils	FASTQ processing utilities		Trimming Sequencing Quality Control		C++	MIT
EagleView	EagleView is an information-rich genome assembler viewer with data integration capability.		Assembly visualization
EagleView genome viewer	EagleView is an information-rich genome assembler viewer with data integration capability.		Viewer
EBCall	EBCall is a software package for somatic mutation detection (including InDels). EBCall uses not only paired tumor/normal sequence data of a target sample, but also multiple non-paired normal reference samples for evaluating distribution of sequencing errors, which leads to an accurate mutaiton detection even in case of low sequencing depths and low allele frequencies.
ECHO	Reference-free short read error correction from diploid genomes, with explicit modeling of heterozygous sites.	SNP discovery InDel discovery	Error correction		Python C++	BSD
EDENA	An assembler dedicated to process the millions of very short reads produced by the Illumina Genome Analyzer.		Assembly
EdgeR	edgeR is an R/Bioconductor software package for statistical analysis of replicated count data. Methods are designed for assessing differential expression in comparative RNA-Seq experiments, but are generally applicable to count data from other genome-scale platforms (ChIP-Seq, MeDIP-Seq, Tag-Seq, SAGE-Seq etc).	RNA-Seq RNA-Seq Quantitation ChIP-Seq Gene Expression Analysis DNA methylation	Statistical testing		R	LGPL	Windows Mac OS X UNIX
ELAND	Efficient Large-Scale Alignment of Nucleotide Databases. Whole genome alignments to a reference genome. Written by Illumina author Anthony J. Cox for the Solexa 1G machine.		Alignment			Commercial
EMBF	Frequency-based, de novo short-read clustering method that organizes erroneous short sequences originating in a single abundant sequence into a tree structure; in this structure, each “child” sequence is considered to be stochastically derived from its more abundant “parent” sequence with one mutation through sequencing errors.		Mapping
Epigenome	A bioinformatic pipeline that scores epigenetic alterations according to strength and significance and links them to potentially affected genes.	Epigenomics	Bisulfite mapping		R Python
EpiGRAPH	EpiGRAPH enables biologists to analyze genome and epigenome datasets with powerful statistical and machine learning methods. In a typical workflow, the user uploads a set of genomic regions of interest (e.g. experimentally mapped enhancers, hotspots of epigenetic regulation or sites exhibiting disease-specific alterations), and EpiGRAPH searches a large database of (epi-) genomic attributes for significant overlap and correlation with the regions in the input dataset. Furthermore, EpiGRAPH can predict the status of genomic regions that were not included in the input dataset.	Epigenomics	Statistics Machine Learning				browser based
ERANGE	ERANGE is a Python package for doing RNA-seq and ChIP-seq.	RNA-Seq Alignment RNA-Seq Quantitation ChIP-Seq Allele-specific transcription		RNAseq analysis Chipseq analysis	Python
ERDS	ERDS is a free, open-source software, designed for detection of copy number variants (CNVs) on human genomes from next generation sequence data. It uses paired Hidden Markov models (PHMM) based on the expected distribution of read depth of short reads and the presence of heterozygous sites. ERDS is NOT good for whole exome data.	Copy number estimation	Hidden Markov Model
ERNE	Extended Randomized Numerical alignEr for accurate alignment of NGS reads. It can map bisulfite-treated reads.	Genomics Alignment Bisulfite Sequencing	Mapping Bisulfite mapping	Bisulfite sequencing sequence alignment	C++	GPL v3	Linux Mac OS X Windows
Error Correction Evaluation Toolkit	Evaluation of error correction results	Sequence Quality Control			Python Perl		POSIX
Est2assembly	Processes raw sequence data from Sanger or 454 sequencing into a hybrid de-novo assembly, annotates it and produces GMOD compatible output, including a SeqFeature database suitable for GBrowse.	RNA-Seq Alignment Genomics	Assembly
ESTcalc	Estimation of project costs for RNA-Seq study.	RNA-Seq	Cost estimation		Perl
EULER	EULER-SR is a program for de novo assembly of reads. Contrary to the overlap-layout approach, EULER-SR uses a de Bruijn graph to construct an assembly. The assembly of a genome corresponds to an Eulerian path in the de Bruijn graph. Long (possibly erroneous) reads, and mate-pairs are used to determine parts of the correct Eulerian traversal in the assembly.		Assembly De Bruijn graph		C++ Perl		Linux
ExomeCNV	Identifies copy number variation from targeted exome sequencing data	Targeted resequencing Copy number estimation			R
ExomeCopy	CNV detection from exome sequencing read depth	Exome and Whole genome variant detection Copy number estimation Exome analysis	Hidden Markov Model	simultaneous normalization and segmentation	R	GPL 2.0+	Linux Windows Mac OS X
ExomePicks	ExomePicks is a program that suggests individuals to be sequenced in a large pedigree.
Exonerate	Various forms of alignment (including Smith-Waterman-Gotoh) of DNA/protein against a reference. Authors are Guy St C Slater and Ewan Birney from EMBL. C for POSIX.		Alignment		C	GPL	Linux
FAAST	Flowspace Assisted Alignment Search Tool		Mapping				Linux
FACS	Rapid and accurate classification of sequences as belonging or not belonging to a reference sequence.	Metagenomics	Bloom filters		Perl f	GPLv2	Linux
FastQ Screen	FastQ Screen provides a simple way to screen a library of short reads against a set of reference libraries. It's most common use is as part of a QC pipeline to confirm that a library comes from the expected source, and to help identify any sources of contamination.	Genomics Transcriptomics	Mapping Sequencing Quality Control	Summarises the mapping of a library against a series of reference sequences	Perl	GPLv3	Linux Mac OS X Windows
FastQC	FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines.		Sequencing Quality Control		Java	GPLv3	UNIX Windows
FastQValidator	Checking that FastQ files are follows standards	Quality Control	Sequencing Quality Control		C++
FDM	Detects differential transcription in RNA-Seq data	RNA-Seq Quantitation
FeatureCounts	featureCounts is a read summarization function included in the Rsubread package. This function can very efficiently assign mapped reads to genomic features such as genes, exons and promoters.	Next Generation Sequencing	Read summarization	read summarization	R C	GPLv3	Linux 64 Mac OS X Mac OS X; x86 64
Figaro	Figaro is a software tool for identifying and removing the vector from raw DNA sequence data without prior knowledge of the vector sequence.	Sequencing	K-mer analysis	AMOS	C++ Perl	Artistic License	UNIX
Figaro	Figaro is a software tool for identifying and removing the vector from raw DNA sequence data without prior knowledge of the vector sequence.	Sequencing	K-mer analysis	AMOS	C++ Perl	Artistic License	UNIX
Filter	Produces a filtered version of an sRNA dataset, controlled by several user-defined criteria, including sequence length, abundance, complexity, transfer and ribosomal RNA removal.	General bioinformatics (pipeline)	Filtering	multi-threading	Java	Custom Licence	Linux 64 Windows Mac OS X
FindPeaks 3.1	Findpeaks was developed to perform analysis of ChIP-Seq experiments.	ChIP-Seq	Peak calling			GPLv3
FindPeaks 4.0 (Vancouver Short Read Package)	The Vancouver Short Read Analysis Package (VSRAP) contains the FindPeaks application for Chip-Seq and RNA-Seq analysis, as well as utilities for SNP finding, working with aligned sequence files and a nascent database for storing SNPs across multiple libraries.	Genomics SNP discovery	Peak calling Database Format conversion Alignment Analysis	command line	Java	GPL	Linux Windows Mac OS X
FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads		Assembly Read pre-processing	combining forward and reverse reads	C	Open Source	Linux 64
Flexbar	flexible barcode and adapter processing for next-generation sequencing platforms	Next Generation Sequencing Sequence Quality Control Genomics	Read pre-processing Sample Barcoding Adapter Removal (software) Trimming	Paired read support separate barcode reads multi-threading	C++	GPLv3	Linux Windows Mac OS X
Flower	Tool for reformatting SFF files into other formats or tab-delimited				Haskell
FlowSim	Tool for simulating errors in 454 sequencing data		Error correction Simulation		Haskell
Flux	FluxCapacitor s a computer program to predict splice form abundancies from reads of an RNA-seq experiment. FluxSimulator can generate simulated data for testing RNA-seq pipelines	RNA-Seq	Simulation
Forge	De novo assembly using a combination of next-generation and Sanger reads	Genomics De-novo assembly	Assembly
FragGeneScan	Application for finding (fragmented) genes in short reads	Metagenomics			C Perl	GPL
FrameDP	Sensitive peptide detection on noisy matured sequences. A self-training integrative pipeline for predicting CDS in transcripts which can adapt itself to different levels of sequence qualities.	RNA-Seq
FreClu	a frequency-based, de novo short-read clustering method that organizes erroneous short sequences originating in a single abundant sequence into a tree structure; in this structure, each “child” sequence is considered to be stochastically derived from its more abundant “parent” sequence with one mutation through sequencing errors. The root node is the most frequently observed sequence that represents all erroneous reads in the entire tree, allowing the alignment of the reliable representative read to the genome without the risk of mapping erroneous reads to false-positive positions.	RNA-Seq Alignment	Mapping
Freebayes	Bayesian genetic variant detector (SNPs, indels, MNPs)	Genomics				MIT
FREEC	A tool for control-free copy number alteration (CNA) detection using deep-sequencing data, particularly useful for cancer studies.	Copy number estimation					Linux Linux 64 Windows
FusionAnalyser	FusionAnalyser is a new graphical, event-driven tool dedicated to the identification of driver fusion rearrangements in human cancer through the analysis of paired-end high-throughput transcriptome sequencing data.	High-throughput sequencing	Gene fusions discovery.	Advanced and user-friendly analysis of RNA-seq data for fusion discovery	C#	GPLv3	Windows Linux
FusionCatcher	FusionCatcher searches for novel/known fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq).	RNA-Seq Fusion finding	Alignment		Python	GPL v3	*NIX
FusionHunter	Identifies gene fusions in RNA-Seq data	RNA-Seq Fusion transcripts			Perl C		Linux Linux 64
FusionMap	Detects fusion events in both single- and paired-end datasets from either RNA-Seq or gDNA-Seq studies and characterize fusion junctions at base-pair resolution.	Fusion genes Fusion transcripts	Split-read		C#	Commercial Freeware	Windows Linux Linux 64
FusionSeq	Identifies fusion transcripts from paired end RNA-Seq data.	Fusion transcripts RNA-Seq Fusion genes	Alignment Analysis		C	Creative Commons - Attribution; Non-commercial 2.5	Mac OS X UNIX Linux
Fuzzypath	Assembler	Genomics	De Bruijn graph Assembly
G-Mo.R-Seq	G-Mo.R-Se is a method aimed at using RNA-Seq short reads to build de novo gene models.	RNA-Seq Alignment				CeCILL	Linux
G-SQZ	Huffman coding-based sequencing-reads specific representation scheme that compresses data without altering the relative order.		Read storage Data compression		C++
Galign	Identifies polymorphisms between sequence reads obtained using Illumina/Solexa technology and a reference genome	SNP discovery	Mapping			GPL
Gambit	A cross-platform GUI for sequence visualization and analysis.		Visualization			GPL 2.0+ Commercial
GAMES	GAMES (Genomic Analysis of Mutations Extracted by Sequencing) is a tool for mining and prediction of functional effect of mutation.	SNP discovery SNP Annotation InDel discovery			Perl		Linux
GASSST	Fast and accurate aligner for short an long reads		Alignment Mapping	Gapped alignment short and long reads	C++	CeCILL	Linux
GASV	Software for classification and comparison of structural variants measured via paired-end sequencing and/or array-CGH.	Structural variation				GPLv3
GATK	The Genome Analysis Toolkit (GATK) is a structured programming framework designed to enable rapid development of efficient and robust analysis tools for next-generation DNA sequencers. The GATK solves the data management challenge by separating data access patterns from analysis algorithms, using the functional programming philosophy of Map/Reduce	SNP discovery	MapReduce Programming Library Localized reassembly/realignment		Java Python
GBrowse	Genome Viewer		Visualization	Genome Viewer	Perl	Open Source	Linux Mac OS X Windows
GeeFu	Database tool for genomic assembly and feature data	Genomics	Assembly		Ruby
GEM	GEM is a java software tool to analyze transcription factor binding ChIP-Seq/ChIP-exo data. It predicts binding events, performs de novo motif discovery and use the motif to improve the binding event calling. It calls binding events right at (or very close to ) the motif positions, deconvolves closely spaced homotypic binding events and accurately discovers binding motifs.	ChIP-Seq Analysis Transcription Factor Binding Site identification Regulatory genomics epigenomics Genomics	Peak calling Peak finding Peak detection Motif discovery K-mer analysis	probabilistic mixture model motif prior multi-threading	Java	Commercial Freeware	Cross-Platform
GEM library	A set of very optimized tools for indexing/querying huge genomes/files. Provided so far: a very fast exact mapper, and an unconstrained split-mapper		Mapping Programming Library Colorspace		C Python OCaml	GPLv3
GENE-Counter	GENE-counter is a computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression	RNA-Seq					Linux Mac OS X
Geneious	Search, organize and analyze genomic and protein information of any size via desktop program that provides publication ready images to enhance the impact of your research.	Phylogenetics Sequence analysis De-novo assembly Whole Genome Resequencing Alignment Systems biology Comparative genomics SNP discovery InDel discovery Transcription Factor analysis Genomics Population genetics Homology Metagenomics Read alignment Structural variation RNA-Seq Motif analysis	Alignment Assembly Assembly validation Annotation Multiple sequence alignment viewer Motif analysis Genetic variation annotation Basecaller Genome browser Sample Barcoding Database Mapping Visualization		Java	Commercial Freeware	Windows Mac OS X Linux Solaris
GeneProf	GeneProf is a web-based, graphical software suite and database resource for high-throughput-sequencing experiments (RNA-seq and ChIP-seq).	Functional Genomics RNA-Seq ChIP-Seq	Workflow Quality Control Alignment Visualization Peak finding Differentially expressed gene identification	User-friendly wizards tutorials examples very flexible reproducible transparent extensible API	Java Javascript	Commercial Freeware	browser based
GeneTalk	GeneTalk, a web-based platform, can filter, reduce and prioritize human sequence variants from NGS data and assist in the time consuming and costly interpretation of personal variants in clinical context. It serves as an expert exchange platform for clinicians and scientists who are searching for information about specific sequence variants and connects them to share and exchange expertise on variants that are potentially disease-relevant.		Genetic variation annotation Sequence variation analysis Variant Calling Structural variation discovery Filtering Annotation Database Exome analysis Sequence analysis Variant Classification Viewer	Easy-to-use point-and-click web interface data visualization data filtering Fast SNP annotation SNP calling Variant annotation and analysis variant counting	Ruby Javascript	Freemium
Genomatix Mining Station (GMS)	The Genomatix Mining Station (GMS) offers mapping of NGS reads onto genomes, transcriptomes and splice-junction libraries. It is a client-server based solution and can be controlled through an intuitive GUI or via command-line. It covers different tasks such as, as genomic positioning, SNP detection, splice analyses and genomic enrichments.	RNA-Seq SNP discovery ChIP-Seq	Assembly Mapping SNP calling Genomic correlations	Client-server based system allows for command-line and web-based access. Grid engine is used for job scheduling and mapping is run on multiple cores. Can be combined with a Genomatix Genome Analyzer (GGA) for a fully integrated NGS solution.	C++ Java Flash	Commercial	Windows Mac OS X Linux
Genome Trax	Genome Trax™ enables you to identify human genome variations of functional significance by mapping your NGS data to known elements such as disease mutations and regulatory sites.	Structural variation Mutations Regulatory sites				Commercial
GenomeBrowse	A free genome browser for exploring sequencing pile-up and coverage data with numerous annotation tracks hosted on the cloud.	Sequence analysis DNA-Seq Alignment De novo sequencing Exome analysis Exome and whole genome variant detection Genetics Whole Genome Resequencing Next Generation Sequencing Genomics	Alignment viewer Assembly visualization Visualization				Windows Linux Mac OS X
Genomedata	Genomedata is a format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint.	Storage	Signal		Python C	GPL	Linux Mac OS X
GenomeJack	GenomeJack is a genome browser specialized in next-generation sequencing data. Advantages are intuitive interface and smooth drag'n drop response.	Genomics Personal genomics	Visualization		Java	Freeware	Windows Mac OS X Linux
GenomeMapper	GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single reference.		Alignment Mapping
Genometa	Genometa is a Java based local bioinformatics program which allows rapid analysis of metagenomic short read datasets. Millions of short reads can be accurately analysed within minutes and visualised in the browser component. A large database of diverse bacteria and archaea has been constructed as a reference sequence.	Metagenomics Genomics	Mapping Visualization	mapping Data Visualisation	Java		Linux Mac OS X Windows
GenomeTools	The GenomeTools genome analysis system is a free collection of bioinformatics tools for genome informatics.1.3.6	Genomics		Integrated solution	C	BSD	POSIX Linux Mac OS X OpenBSD Windows (Cygwin) UNIX
GenomeView	GenomeView is a next-generation stand-alone genome browser and editor initiated in the BSB group at VIB and currently developed at Broad Institute. It provides interactive visualization of sequences, annotation, multiple alignments, syntenic mappings, short read alignments and more. Many standard file formats are supported and new functionality can be added using a plugin system.	Genomics Comparative genomics Comparative transcriptomics Transcriptomics Gene annotation retrieval Quality Control Sequencing Sequence analysis	Visualization Alignment viewer Multiple sequence alignment viewer Viewer Genome browser	Visualization of a multitude of genomics data	Java	GPL	platform-independent
GenomicTools	GenomicTools is a flexible computational platform for the analysis and manipulation of high-throughput sequencing data such as RNA-seq and ChIP-seq. A variety of mathematical operations between sets of genomic regions is implemented thereby enabling the prototyping of computational pipelines that can address a wide spectrum of tasks from preprocessing and quality control to meta-analyses. More specifically, the user can easily create average read profiles across transcriptional start sites or enhancer sites, quickly prototype customized peak discovery methods for ChIP-seq experiments, perform genome-wide statistical tests such as enrichment analyses, design controls via appropriate randomization schemes, among other applications.	Genomics ChIP-Seq RNA-Seq	Genomic overlaps Peak detection Profiles Heatmaps	create custom pipelines feature overlaps identify binding site peaks in ChIP-seq data create read profiles create read heatmaps	C C++	GPL 2
GenoMiner	A proprietary NGS analysis solution. Powerful hardware comes with preinstalled software, organized in workflows.	Reference assembly De-novo assembly ChIP-Seq RNA-Seq	Assembly Viewer Error correction Mutation detection Peak detection Expression profiling Sequence alignment	GenoMiner provide workflows for Reference assembly De novo assembly ChIPSeq RNASeq and more. You upload your files at the beginning and you get the results at the end while you can choose from various tools to use for analysis.	Java	Commercial	Linux
GenoViewer	A feature rich NGS assembly viewer/browser.		Viewer	large file loading multicontig handling SNP/InDel/Read Error display and search mutation table generation and export consensus sequence generation and export	Java	Freeware	platform-independent
GensearchNGS	A user friendly framework for re-sequencing in a diagnostics context: searching for mutations/variants, especially on well known genes.	Targeted resequencing	Alignment Alignment viewer Read Alignment Variant Prioritization Mutation detection Database Database submission preparation	Plugin framework Cafe Variome submission	Java	Commercial	UNIX Windows
GenVision	GenVision is a genomic visualization software package that is fully integrated with Lasergene and is designed to support easy generation of publication quality graphics and maps.	Genomics	Visualization			Commercial	Windows Mac OS X
Geoseq	Instead of mapping the reads to reference genomes or sequences, Geoseq maps a reference sequence against the sequencing data. It is web-based, and holds pre-computed data from public libraries.	Resequencing	Mapping
GigaBayes	A short-read SNP and short-INDEL discovery program.	Genomics SNP discovery	SNP calling
GimmeMotifs	GimmeMotifs is a de novo motif prediction pipeline, especially suited for ChIP-seq datasets. It incorporates several existing motif prediction algorithms in an ensemble method to predict motifs and clusters these motifs using the WIC similarity scoring metric.	Transcription regulation ChIP-Seq Epigenomics	Motif analysis		Python	MIT	Linux
Girafe	The R/Bioconductor package girafe facilitates the functional exploration of alignments of sequence reads from next-generation sequencing data to a genome. It allows users to investigate the genomic intervals together with the aligned reads and to work with, visualise and export these intervals.		Alignment		R
Gk arrays	Gk-arrays are a data structure to index the k-mers in a collection of reads.	Genomics Transcriptomics Metagenomics	Assembly Error correction Mapping	programming library	C++	CeCILL-C license	Linux Linux 64 Mac OS X any
GMAP	GMAP (Genomic Mapping and Alignment Program) for mRNA and EST Sequences.		Alignment Mapping		C Bourne shell		UNIX
Gnumap	The Genomic Next-generation Universal MAPper (gnumap) is a program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size. Currently, gnumap is designed to be used with the _int.txt data received from the Solexa/Illumina machine.		Mapping		C++
Goby framework	Goby is a next-gen data management framework designed to facilitate the implementation of efficient next-gen data analysis pipelines.	RNA-Seq	Programming Library Data compression		Java	GPLv2
Golden Helix	Golden Helix is a bioinformatic software provider and analytic service provider. The core of its business is about empowering scientists to discover more, discover it easier, and to come away with valid and reproducible bioinformatics results. The software, SNP & Variation Suite, is a stable platform for clever data manipulations, robust quality assurance, advanced statistical modeling, and compelling visual results in a genome browser environment of DNA Seq, Copy Number variation, SNP Chip, and RNA Seq data.	Epigenomics Genomics DNA-Seq SNP discovery Whole Genome Resequencing Analysis Copy number estimation Quality Control	Quality Control Statistics Statistical testing Genome browser Annotation Filtering Collapsing Methods Variant Classification Variant Mapping				Windows Linux Mac OS X
Goseq	An R package to detect Gene Ontology (GO) categories and other categories of genes (such as KEGG pathways) that are over/under represented in an RNA-seq data.	RNA-Seq Quantitation	Gene Set Testing		R	LGPL	UNIX Windows
Gowinda	Gowinda: unbiased analysis of gene set enrichment for Genome Wide Association Studies	Genomics Genome Wide Association Studies Population genetics Population Genomics High-throughput sequencing	Gene set enrichment Gene ontology Genome wide association studys	Multicore	Java	Mozilla Public License	Mac OS X Linux Windows
GPS	GPS is a high spatial resolution peak detection algorithm for ChIP-Seq data.	Genomics ChIP-Seq Transcription Factor Binding Site identification Regulatory genomics epigenomics	Protein Binding Peak Detection	multi-threading	Java	Commercial Freeware	Cross-Platform
GPSeq	Analyze RNA-seq data to estimate gene and exon expression, identify differentially expressed genes, and differentially spliced exons	RNA-Seq Quantitation			R C
GRS	Reference-based data compression for storage of resequencing data		Data compression	sequence compression	C Bourne shell	Commercial Freeware	Linux Linux 64
GSNAP	GSNAP can align both single-end and paired-end reads as short as 14 nt and of arbitrarily long length. It can detect short- and long-distance splicing, including interchromosomal splicing, in individual reads using probabilistic models or a database of known splice sites. Our program also permits SNP-tolerant alignment to a reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite treated DNA for the study of methylation state.	RNA-Seq Alignment DNA methylation	Mapping Bisulfite mapping		C Perl
Hairpin Annotation	Generates a secondary structure from an RNA sequence and highlights regions of interest using RNAplot	General bioinformatics (pipeline)			Java	Custom Licence	Linux 64 Windows Mac OS X
Haplowser	Haplowser: comparative haplotype browser for personal genome and metagenome		Visualization Haplotype reconstruction		Java	GPL
HawkEye	An interactive visual analytics tool for genome assemblies.		Assembly visualization	Assembly visualization	C++	Artistic License	Linux Mac OS X
HeliSphere	Open-source LINUX software package intended for use in analyzing data produced by the HeliScope Single Molecule Sequencer.	Genomics Whole Genome Resequencing RNA-Seq SNP discovery	Mapping			Freeware	Linux
HI	Program for haplotype reconstruction from paired-end reads.		Haplotype reconstruction		Java
Hicup	A mapping pipeline for HiC interaction data. Performs independent mapping on each end of the interaction pair and removes commonly found artefacts.	Epigenomics	Mapping		Perl	GPLv3	UNIX Linux Mac OS X
HiTEC	An algorithm which provides a highly accurate, robust, and fully automated method to correct reads produced by high-throughput sequencing methods.		Error correction		C++	GPLv3	Linux
HMMSplicer	Splice junction discovery in RNA-Seq data	RNA-Seq Alignment			Python
HPeak	Hidden Markov model (HMM)-based Peak-finding algorithm for analyzing ChIP-Seq data to identify protein-interacting genomic regions.	ChIP-Seq	Hidden Markov Model
HTSeq	Python framework to process and analyse high-throughput sequencing (HTS) data		Programming Library		Python	GPLv3
Hybrid-SHREC	Improves sequence data quality using information from multiple platforms.		Error correction		Java
IBD2	Our algorithm uses a non-homogeneous hidden Markov model (HMM) that employs local recombination rates to identify chromosomal regions that are identical by descent (IBD=2) in children of consanguineous or non-consanguineous parents solely based on genotype data of siblings derived from high-throughput sequencing platforms.	Targeted resequencing			R Java
Ibis	Ibis (Improved base identification system), is an accurate, fast and easy-to-use base caller for the Illumina sequencing system, which significantly reduces the error rate and increases the output of usable reads. Ibis is faster and makes fewer assumptions about chemistry and technology	Sequencing	Basecaller	Statistical learning of base calling parameters and calibrated quality scoring	Python C C++	Non-commercial	Linux Windows (Cygwin)
ICORN	Iteratively aligns deep coverage of short sequencing reads to correct errors in reference genome sequences and evaluate their accuracy.		Assembly Sequencing Quality Control
IDBA	IDBA (Iterative De Bruijn graph short read Assembler) is a short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system	De-novo assembly	Assembly				POSIX Linux Linux 64
IGV	The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated datasets. It supports a wide variety of data types and format, including short-read alignments in the SAM/BAM format. Data can be viewed from local files or over the web via http.	Genomics	Visualization		Java	LGPL	Windows Mac OS X Linux
Illuminator	Software for machines running Windows to identify variants in Illumina short read data.	SNP discovery InDel discovery
Inchworm	Employs the Kmer graph method to reconstruct (in many cases full-length) transcripts from Illumina RNA-Seq (preferrably strand-specific) reads.	RNA-Seq De novo transcriptome assembly
InGAP	inGAP is an integrated platform for next-generation sequencing project, the core function of which is to detect SNPs and indels using a Bayesian algorithm.	SNP discovery	Mapping Assembly visualization
Ingenuity Variant Analysis	Ingenuity Variant Analysis is a web application that helps researchers studying human disease to identify causal variants from human resequencing data in just minutes. Ingenuity Variant Analysis combines analytical tools and integrated content to help you rapidly identify and prioritize variants by drilling down to a small, targeted subset of compelling variants based both upon published biological evidence and your own knowledge of disease biology. With Variant Analysis, you can interrogate your variants from multiple biological perspectives, explore different biological hypotheses, and identify the most promising variants for follow-up.	Genomics Genetics Next Generation Sequencing Exome and Whole genome variant detection Whole Genome Resequencing Analysis Exome analysis Causal Variant Detection Targeted Sequencing	Biological Interpretation and Analysis of DNA Sequence Data
Integrated Genome Browser	Visualization software for next-generation genomics	Genomics	Visualization		Java	Open Source	platform-independent
IOmics	iOmics is a cloud based workflow analysis framework for managing, analyzing and visualizing NGS data.	Genomics Transcriptomics Epigenomics RNA-Seq Exome and Whole genome variant detection	Genome Alignment Assembly Ab-inito gene prediction Genetic variation annotation Exome analysis ChIP seq MiRNA analysis (Ref and Ab-initio)			Commercial	cloud
IQSeq	Integrated Isoform Quantification Analysis based on A Partial Sampling Framework	RNA-Seq Quantitation Alternative Splicing			C++
Isas	Fast aligner for color and base space short read data.		Alignment Colorspace				Linux
IsoEM	Expectation maximization algorithm for estimating alternative splicing isoform frequencies	Alternative Splicing	Expectation Maximization		Java
ISSAKE	Short Sequence Assembly by K-mer search and 3' read Extension, Immunology version (iSSAKE)	Metagenomics	Assembly		Perl Python	GPLv2
JBrowse	Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.		Visualization		Perl Javascript	Open Source	browser based
Jellyfish	Fast, memory-efficient k-mer counting algorithm				C++	GPLv3	Linux 64 Mac OS X
JointSLM	Copy number estimation from read depth information	Copy number estimation			R
KARMA	K-tuple Alignment with Rapid Matching Algorithm	Bisulfite Sequencing	Mapping
Kismeth	Web-based tool for bisulfite sequencing analysis	DNA methylation Epigenomics	Bisulfite mapping
Kissnp	kisSnp compares two sets of NGS raw reads, detecting Single Nucleotide Polymorphism occurring between the two sets. The two sets typically come from the sequencing of two individuals from the same species or from closely related species.	Comparative genomics Comparative transcriptomics Gene annotation retrieval SNP discovery InDel discovery	Micro assembly De Bruijn graph	SNP calling	C	CeCILL	Linux
KNIME	Software for organizing bioinformatic workflows		Workflow			GPLv3	Windows Mac OS X Linux
Knime4Bio	custom nodes for the interpretation of Next Generation Sequencing data with KNIME.	Genomics Gene annotation retrieval Mutations and regulatory sites		KNIME	Java	GPLv3	any
Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Metagenomics	Visualization	Interactive Animation HTML5 canvas graphics	Javascript Perl		Linux UNIX Mac OS X
Lab7	Data workflow management platform to streamline NGS analyses	Genomics	Workflow		Python Javascript	Commercial	Mac OS X Linux
Lasergene	Lasergene is a comprehensive DNA and protein sequence analysis software suite comprised of seven applications which include functions ranging from sequence assembly and SNP detection, to automated virtual cloning and primer design.	Alignment De novo sequencing De-novo assembly Genomics InDel discovery Integrated solution Mapping Phylogenetics Protein structure analysis Read alignment SNP discovery Sequence analysis Transcription Factor Binding Site identification	Alignment Alignment Analysis Annotation Assembly Chromatogram viewer Colorspace Sequence analysis Integrated Solution Mapping PCR Primer Design Paired End Scaffolding			Commercial	Windows Mac OS X
LAST	Short read alignment program incorporating quality scores	Genomics Comparative genomics	Alignment		C++	GPLv3
LASTZ	A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically	Genomics	Mapping Alignment				Mac OS X Linux
LobSTR	lobSTR is an alignment and genotyping tool for profiling short tandem repeats from next generation sequencing data	Sequencing	Profiling short tandem repeats from short reads	Fast Scalable sequence alignment Gapped alignment	C++ R Python	Freeware	UNIX
LOCAS	LOCAS low-coverage short-read assembler		Assembly		C++		Linux
LookSeq	AJAX-based browser for deep sequencing data		Assembly visualization
MACS	Model-based Analysis of ChIP-Seq data.	ChIP-Seq	Peak calling		Python	Artistic License	platform-independent
MagicViewer	Large-scale short reads and sequencing depth visualization.	De novo sequencing Targeted resequencing	Visualization Genetic variation annotation		Java		platform-independent
MapDamage	Identifies and quantifies DNA damage patterns in ancient DNA	Ancient DNA	Quality Control Statistical Modelling		Python/R		Linux Mac OS X
MapNext	MapNext provides four mainly analysis: (i) unspliced alignment and clustering of reads, (ii) spliced alignment of transcriptomic reads, (iii) SNP detection and calculation of SNP frequency from population sequences, and (iv) storage of result data into database to make it available for more flexible query and further analyses.	SNP discovery RNA-Seq Alignment	Alignment		C++ Perl
Mapsembler	Mapsembler is a targeted assembly software. It takes as input a set of NGS raw reads and a set of input sequences (starters). It first determines if each starter is read-coherent, e.g. whether reads confirm the presence of each starter in the original sequence. Then for each read-coherent starter, Mapsembler outputs its sequence neighborhood as a linear sequence or as a graph, depending on the user choice.	Metagenomics Transcriptomics DNA-Seq RNA-Seq Quantitation Targeted assembly	Assembly Micro assembly Mapping	De novo assembly Identify Novel Exons Remove contaminants Detect enzymes in metagenomics NGS reads	C	CeCILL	Linux
MapSplice	We introduce a second generation splice detection algorithm, MapSplice, whose focus is high sensitivity and specificity in the detection of splices as well as CPU and memory efficiency. MapSplice can be applied to both short (<75 bp) and long reads (75 bp). MapSplice is not dependent on splice site features or intron length, consequently it can detect novel canonical as well as non-canonical splices. MapSplice leverages the quality and diversity of read alignments of a given splice to increase accuracy.	RNA-Seq Alignment	Mapping		C++ Python		Linux
MapView	Visualization of short reads alignment on desktop computer		Visualization				Linux Windows
MAQ	Mapping and Assembly with Qualities (renamed from MAPASS2). Particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has preliminary functions to handle ABI SOLiD data.	Genomics SNP discovery	Mapping		C++ Perl	GPL
MAQGene	Complete pipeline for mutant discovery, with web front end	SNP discovery	Mapping Integrated Solution
MARGARITA	SNP discovery and genotyping from low-coverage sequencing data	SNP discovery Genotyping
Mason	A fast, feature-rich and hackable read simulator for the simulation of NGS and Sanger data.	Genomics	Simulation Assembly Mapping	Empirical or simple model for position dependent errors can write out sample position and extensive information about the sampled infix haplotype simulation through mutation of reference sequence.	C++	GPLv3	UNIX Windows
Mauve	Mauve Genome Alignment software, for comparing two or more draft or finished genomes	Comparative genomics Genomics Transcriptomics	Genome Alignment Alignment Visualization Assembly QC		C++ Java	GPL	Mac OS X Windows Linux
MAXIMUS	Hybrid reference and de novo assembly pipeline	Genomics	Hybrid assembly
MAYDAY	Extensible platform for visual data exploration and interactive analysis and provides many methods for dissecting complex transcriptome datasets.	RNA-Seq	Visualization
MEGAN	Metagenome Analysis Software - MEGAN (“MEtaGenome ANalyzer”) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.	Metagenomics		metagenomic analysis functional classification		Commercial Freeware
Megraft	Megraft is a software tool to graft ribosomal small subunit (16S/18S) fragments from metagenomes onto full-length SSU sequences, enabling accurate diversity estimates from fragmentary and non-overlapping sequence data.	Metagenomics Phylogenetics Sequence analysis Community analysis Rarefaction	Hidden Markov Model Sequence analysis		Perl	GPLv3	Linux UNIX Mac OS X
Meraculous	De novo genome assembler from short reads		Assembly	De novo assembly scaffolding	Perl C
METAGENassist	User-friendly, web-based analytical pipeline for comparative metagenomic studies. Input can be derived from either 16S rRNA data or NextGen shotgun sequencing.	Metagenomics	Visualization Statistics Clustering Machine Learning	Easy-to-use point-and-click web interface; data visualization; publication-quality graphs and charts; wide variety of statistical methods; taxon-to-phenotype mapping; data filtering and normalization; supports many common input formats
MetaSim	The software can be used to generate collections of synthetic reads.	Metagenomics Genomics	Simulation Assembly Mapping		Java	Commercial Freeware
Metaxa	Metaxa uses Hidden Markov Models to identify, extract and classify small-subunit (SSU) rRNA sequences (12S/16S/18S) of bacterial, archaeal, eukaryotic, chloroplast and mitochondrial origin in metagenomes and other large sequence sets	Metagenomics Phylogenetics Sequence analysis Community analysis	Hidden Markov Model Sequence analysis		Perl	GPLv3	Linux UNIX Mac OS X
MethMarker	MethMarker facilitates the design of DNA methylation assays for COBRA, bisulfite SNuPE, bisulfite pyrosequencing, MethyLight and MSP. It also implements a systematic workflow for design, optimization and (computational) validation of DNA methylation biomarkers. This workflow starts from a preselected differentially methylated region (DMR) and results in an optimized DNA methylation assay that is ready to be tested in a large-scale clinical trial.	Epigenomics DNA methylation			Java		Windows Linux Mac OS X Solaris
MethylCoder	Pipeline for fast, simple processing of BiSulfite-treated reads into methylation data. Includes scripts for analysis and visualization. In addition to a binary output, the direct output of methylcoder is a text file that indicates per-nucleotide methylation context (CG/CHG/CHH) and methylation levels (both coverage and C-T conversions)	Genomics Sequencing DNA methylation Epigenomics	Mapping Bisulfite mapping		Python C	BSD	Linux Linux 64 Mac OS X
MetMap	Produces corrected site-specific methylation states from MethylSeq experiments and annotates unmethylated islands across the genome.	DNA methylation
MeV	Visualization of genomic data, Differential Gene Expression based on DEGseq, DESeq and edgeR	RNA-Seq	Clustering Visualization Classification Differentially expressed gene identification			Artistic License
MG-RAST	MG-RAST is a fully-automated service for annotating metagenome samples.	Metagenomics Phylogenetics Metabolic reconstruction	Annotation
MicroRazerS	MicroRazerS is a tool optimized for mapping short RNAs onto a reference genome.		Mapping		C++		Linux
Microsoft Biology Foundation	C#/.NET library for biological applications.		Programming Library		C#
MICSA	Combines positional information with information on motif occurrences to better predict binding sites of transcription factors (TFs)	ChIP-Seq	Motif analysis
Minia	De novo assembly of human genomes on a desktop computer	De novo assembly	Assembly	Memory efficient and fast	C++	CeCILL	Linux Mac OS X
MIP Scaffolder	MIP Scaffolder is a program for scaffolding contigs produced by fragment assemblers using mate pair data.		Scaffolding		C++ Perl		Linux
MIRA	MIRA 3 - Whole Genome Shotgun and EST Sequence Assembler	De-novo assembly SNP discovery RNA-Seq Alignment	Smith-Waterman Graph reduction Learning algorithm Assembly Mapping K-mer analysis		C++	GPL	Linux Mac OS X UNIX
MiRanalyzer	Web-server for identifying and analyzing miRNA in next-gen sequencing experiments	MiRNA		Annotation of micro RNA differential expression	Java Perl		browser based
MiRCat	Predicts mature miRNAs and their precursors from an sRNA dataset and a genome.	General bioinformatics (pipeline)	MiRNA Prediction	Detection and prediction of known or novel miRNAs secondary structure generation	Java	Custom Licence	Linux 64 Windows Mac OS X
MiRDeep	Discovering known and novel miRNAs from deep sequencing data	MiRNA			Perl
MiRNAkey	A software pipeline for the analysis of microRNA Deep Sequencing data	MiRNA			Java Perl		Linux Mac OS X
MiRProf	Determines normalised expression levels of sRNAs matching known miRNAs in miRBase.	General bioinformatics (pipeline)	MiRNA profiling		Java	Custom Licence	Linux 64 Windows Mac OS X
MirTools	Web server for microRNA profiling and discovery based on high-throughput sequencing	Small RNA transcriptome MiRNA			Perl PHP
MISO	An alternative to Cufflinks, MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes.	RNA-Seq Quantitation RNA-Seq
Mlgt	Processing and analysis of high throughput, long-read (e.g. Roche 454) sequences generated from multiple loci and multiple biological samples. Sequences are assigned to their locus and sample of origin, aligned and trimmed. Where possible, genotypes are called and variants mapped to known alleles.	Genotyping Targeted resequencing Resequencing	Sequence analysis Error correction Filtering Sample Barcoding Pooled samples Read Alignment	Sequence assignment sequence alignment allignment error correction variant counting genotype calling allele-matching	R	GPL >=2	Windows UNIX Mac OS X
MMSEQ	Pipeline and methodology for simultaneously estimating isoform expression and allelic imbalance in diploid organisms using RNA-seq data.	Allele-specific transcription			C++		Mac OS X Linux 64
MochiView	Hybrid genome browser and motif visualization/analysis/management desktop software.	Genomics ChIP-Seq ChIP-on-chip RNA-Seq Motif analysis	Genome browser Motif analysis	Desktop hybrid genome browser and motif visualization/analysis software	Java		Linux Mac OS X Windows
MoDIL	Program to detect small indels in next generation sequencing data	Genomics InDel discovery			Python
MOM	Short-read mapping	Genomics	Mapping
MOSAIK	Reference guided aligner/assembler.		Assembly Colorspace		C++	Commercial GPLv2	Windows Linux Mac OS X
MPscan	MPscan (multi-pattern scan) is a program for mapping short reads (<30bp) exactly on a set of reference sequences (eg, a genome) without indexing the reference. MPscan performs only exact mapping (no substitution, nor indels), is fast (optimal complexity), and easy to use.	Genomics Transcriptomics	Mapping		C++		Linux Mac OS X
MrCaNaVaR	mrCaNaVaR is a copy number caller that analyzes the next-generation sequence mapping read depth to discover large segmental duplications and deletions. It also has the capability of predicting absolute copy numbers of genomic intervals.	Genomics Personal genomics Copy number estimation	Read depth analysis		C	Commercial Freeware	POSIX
MrFAST	mrFAST is designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient manner.	Genomics	Read Alignment Mapping		C	BSD	UNIX
MrsFAST	mrsFAST is a micro-read substitution-only Fast Alignment Search Tool. mrsFAST is a cache-oblivous short read mapper that optimizes cache usage to get higher performance.	Genomics	Read Alignment Mapping		C	BSD	UNIX
MTR	Metagenomics software for clustering at multiple ranks.	Metagenomics			C++ Matlab
MU2A	Genomic variant annotation tool	SNP Annotation			Java	Apache License 2.0	Windows Linux Mac OS X
MUMmer	MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. Basically it is a ultra-fast alignment of large-scale DNA and protein sequences	Genomics Transcriptomics	Alignment			Artistic License	Linux
MUMmerGPU	MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by HTS.	Genomics Transcriptomics	Alignment GPU
MuMRescueLite	Probabilistically reincorporates multi-mapping tags into mapped short read data.	Genomics ChIP-Seq	Mapping		Python	MIT
MuSICA 2	Assembles millions of short (36-nucleotide) reads collected from a single flow cell lane of Illumina Genome Analyzer to shotgun-sequence ~800 human full-length cDNA clones.	Clone verification	Assembly		Perl
Mutascope	Mutascope is a software suite designed to analyze data from high throughput sequencing of PCR amplicons, with an emphasis on normal-tumor comparison for the accurate and sensitive identification of low prevalence mutations.	Cancer biology	Somatic variant calling Analysis Pipeline		Perl		UNIX
MuTect	MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.		SNP calling
Myrialign	Software to align short reads produced by a short read genome sequencer to a reference genome. Alignments can contain any number of SNPs, insertions and deletions, up to a user specified cutoff. Myrialign can use a Cell Broadband Engine processor to accelerate alignments if available, for example on a PlayStation 3 running GNU/Linux. Myrialign performs brute force alignment using a variant on the "bitap" algorithm that aligns several thousand reads to a reference in parallel. It uses bit-parallelism, multiple processors, and Cell SPUs if available. Unlike other reference genome alignment software, heuristics and hashtable lookups are not used. Myrialign will find alignments with any number of errors up to a user specified cutoff. The emphasis is on doing a 100% accurate search as fast as is possible.		Mapping Alignment GPU
Myrna	Myrna is a cloud computing tool for calculating differential gene expression in large RNA-seq datasets.	RNA-Seq Quantitation RNA-Seq Alignment	Hadoop MapReduce
Mzip	Reference-based sequence data compression tool		Data compression
Nesoni	Nesoni is a high-throughput sequencing data analysis toolset.	RNA-Seq Alignment SNP discovery Phylogenetics	Alignment	largely for bacterial genomes	Python
Newbler	The assembly/mapping program developed by 454 Life Sciences for of 454 data	De-novo assembly	Assembly Mapping		C++	Unknown	Linux 64
Nexalign	Nexalign is a program to align millions of short reads from next-generation sequencing data sets to reference genomes		Mapping		C++ R	GPL	UNIX
NextGen Utility Scripts	A collection of links to scripts available for working with data generated by new sequencing technologies.			A collection of many different scripts
NextGENe	de novo and reference assembly of Roche/454, Illumina and SOLiD data. Uses a novel Condensation Assembly Tool approach where reads are joined via "anchors" into mini-contigs before assembly which reduces sequencing errors. Requires Win or MacOS.	De novo sequencing Metagenomics SNP discovery InDel discovery Targeted resequencing		Unique condensation tool Data Visualisation very flexible	C++	Commercial	Windows
Ngs backbone	ngs_backbone is a bioinformatic application created to work on sequence analysis by using NGS (Next Generation Sequencing) and sanger sequences. It is capable of cleaning reads, do de novo assembly or mapping against a reference and annotate SNPs, SSRs, ORFs, GO terms and sequence descriptions.	SNP discovery Genomics	Mapping Assembly			AGPL	UNIX
NGS-DesignTools	Tools to assist in designing deep sequencing experiments for haplotype reconstruction and structural variant breakpoint detection	Structural variation RNA-Seq Quantitation	Haplotype reconstruction Simulation
Ngs-pipeline	Complete solution for human re-sequencing projects	Personal genomics Regulatory genomics epigenomics SNP discovery Structural variation discovery Regulatory element annotation InDel discovery	Mapping		Perl	GPLv3	Linux
NGSUtils	NGSUtils is a suite of software tools for working with next-generation sequencing datasets	Genomics Transcriptomics	Filtering QC Read pre-processing Variant Calling Format conversion		Python	GPL	Linux Mac OS X
NGSView	High-throughput sequencing technologies introduce novel demands on tools available for data analysis. We have developed NGSView, a generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface. NGSView is available under an open source license and can be extended through a well documented API.	Genomics	Assembly visualization
NOISeq	Next Generation Sequencing (NGS) technologies are increasingly being used for gene expression pro�filing as a replacement for microarrays. The expression level given by these technologies is the number of reads in the library mapping to a given feature (gene, exon, transcript, etc.), i.e., the read counts. Most of the statistical methods for assessment of differential expression using count data rely on parametric assumptions about the distribution of the counts (Poisson, Negative Binomial, …). Moreover, many of them need replicates to work and tend to have problems to evaluate differential expression in features with low counts. NOISeq is a non-parametric approach for the identification of differentially expressed genes from count data. NOISeq empirically models the noise distribution of count changes by contrasting fold-change differences (M) and absolute expression differences (D) for all the features in samples within the same condition. This reference distribution is then used to assess whether the M-D values computed between two conditions for a given gene is likely to be part of the noise or represent a true differential expression. The are two variants of the method: NOISeq-real uses replicates, when available, to compute the noise distribution and, NOISeq-sim simulates them in absence of replication. It should be noted that the NOISeq-sim simulation procedure assimilates to technical replication and does not reproduce biological variability, which is necessary for population inferential analysis.	Differential Expression
NovelSeq	A computational framework to discover the content and location of long novel sequence insertions using paired-end sequencing data	Structural variation InDel discovery	Mapping Assembly Variant Calling		C	BSD	UNIX
Novocraft	Novoalign is a program for mapping short reads from the Illumina/SOLiD sequencing platform(s) to a reference genome.	Genomics Whole Genome Resequencing RNA-Seq Alignment ChIP-Seq MiRNA	Mapping	Bisulfite sequencing Mate-pair/jumping libraries parallel execution insertions/deletions SAM format output paired-end colourspace MPI	C++	Commercial Freeware	Mac OS X Linux 64
NPS	Identify nucleosome positions given histone-modification ChIP-seq or nucleosome sequencing at the nucleosome level.	Epigenomics ChIP-Seq			Python
NucleR	nucleR is a R/Bioconductor package for working with tiling arrays and next generation sequencing. It uses a novel aproach in this field which comprises a deep profile cleaning using Fourier Transform and peak scoring for a quick and flexible nucleosome calling	ChIP-on-chip ChIP-Seq Nucleosome Positioning Epigenomics	Annotation Peak calling Protein Binding Peak Detection Peak detection Peak finding Programming Library	Multicore Integrated solution	R	LGPL3	Cross-Platform
Oases	De novo transcriptome assembler for very short reads	De novo transcriptome assembly		supports strand specific and paired-end RNA-seq data sets	C	GPLv3
OLego	OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a seeding and extension scheme, and does not rely on a separate external mapper. It achieves high sensitivity of junction detection by using very small seeds (12-14 nt), efficiently mapped using Burrows-Wheeler transform (BWT) and FM-index. This also makes it particularly sensitive for discovering small exons. It is implemented in C++ with full support of multiple threading, to allow fast processing of large-scale data.	Genomics RNA-Seq RNA-Seq Alignment	Mapping Alignment	capable of using very small seeds for splice mapping but still fast and accurate	C++	GPLv3	Linux Linux 64 Mac OS X
Omixon Variant Toolkit	Omixon Target Standard, Target HLA and Target Pro are designed to help clinical, diagnostic and research labs to efficiently get the maximum accuracy and precision from their targeted NGS data.	Comparative genomics Mapping Sequence analysis Read alignment InDel discovery SNP discovery	Alignment Assembly Mapping Colorspace Basespace	easy to use parameters full documentation also a plugin available in CLCbio and Geneious		Commercial Freeware	interoperable
Optimus Primer	Automated primer design for large-scale resequencing by second generation sequencing	Resequencing	PCR Primer Design
PacBio conversion tools	Tools to convert from PacBio HDF5 format to other commonly used formats & libraries to read HDF5 from Java & R		Programming Library Conversion		Java R Python
PaCGeE	PaCGeE (Parallel Computational Genomics Engine) is a suite of HPC accelerated sequence data analysis tools for assembly and analysis. The tool set comprises of many popular open source and proprietary software for a high performance, high throughput and high quality data analysis. The PaCGeE family of parallel NGS analysis tools are Cloud-MAQ, VELVET-P, EULER, ERANGE, BOWTIE, BFAST, MPI-BLAST, ChIP Seq Peak Finder etc		Mapping Hadoop			Commercial
PALMA	We present a novel approach based on large margin learning that combines accurate splice site predictions with common sequence alignment techniques. By solving a convex optimization problem, our algorithm -- called PALMA -- tunes the parameters of the model such that true alignments score higher than other alignments. We study the accuracy of alignments of mRNAs containing artificially generated micro-exons to genomic DNA. In a carefully designed experiment, we show that our algorithm accurately identifies the intron boundaries as well as boundaries of the optimal local alignment. It outperforms all other methods: for 5702 artificially shortened EST sequences from C. elegans and human it correctly identifies the intron boundaries in all except two cases. The best other method is a recently proposed method called exalin which misaligns 37 of the sequences. Our method also demonstrates robustness to mutations, insertions and deletions, retaining accuracy even at high noise levels.	RNA-Seq Alignment	Alignment
PALMapper	Fast and Accurate Spliced Alignments of Sequence Reads.		Mapping		C++	GPLv3
PanGEA	Tool which enables a fast and user-friendly analysis of allele specific gene expression using the 454 technology.	RNA-Seq Allele-specific transcription SNP discovery				Mozilla Public License
PARalyzer	Tool to analyze cross-linking and immunoprecipitation data (CLIP)				Java	Commercial Freeware
Partek Genomics Suite	Easy to use software providing A to Z analysis for all Next Generation Sequencing and Microarray data.	Allele-specific transcription RNA-Seq Quantitation Epigenomics Functional Genomics ChIP-Seq Alternative Splicing SNP discovery Small RNA transcriptome
PASH	Pash 3.0 performs sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-Seq and methylome mapping by whole-genome bisulfite sequencing	Epigenomics DNA methylation	Alignment Bisulfite mapping
PASS	PASS performs fast gapped and ungapped alignments of short DNA sequences onto a reference DNA, typically a genomic sequence. It is designed to handle a huge amount of reads such as those generated by Solexa, SOLiD or 454 technologies. The algorithm is based on a data structure that holds in RAM the index of the genomic positions of seed" words (typically 11-12 bases) as well as an index of the precomputed scores of short words (typically 7-8 bases) aligned against each other.		Alignment		C++		Linux Windows
Patchwork	Patchwork is a bioinformatic tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes. High quality results are obtained even if samples have low coverage, ~4x, low tumor cell content or are aneuploid. Patchwork is available in two formats. The first, named simply patchwork, takes BAM files as input whereas patchworkCG takes input from CompleteGenomics files. Detailed guides and information regarding these can be found in their respective tabs.	Copy number estimation (Allele-specific!)	Structural variation discovery	Allele specific copy numbers.	R		Linux Mac OS X
PatMaN	Patman searches for short patterns in large DNA databases, allowing for approximate matches. It is optimized for searching for many small pattern at the same time, for example microarray probes.		Mapping
PE-Assembler	A simple 3' extension approach to assembling paired-end reads and capable of parallelization	De-novo assembly	Scaffolding		C++
PeakAnalyzer	PeakAnalyzer is a set of applications for processing ChIP signal peaks.	Functional Genomics	ChIP-Seq analysis		Java C++ R
PeakRanger	A multi-purpose, ultrafast ChIP Seq peak caller	ChIP-Seq	Peak calling		C++	Artistic License	Linux Mac OS X
PeakSeq		ChIP-Seq			C Perl
PECAN	Alignment method practical for large genomic sequences.		Alignment
PEMer	The package is composed of three modules, PEMer workflow, SV-Simulation and BreakDB. PEMer workflow is a sensitive software for detecting SVs from paired-end sequence reads. SV-Simulation randomly introduces SVs into a given genome and generates simulated paired-end reads from the ‘novel’ genome. Subsequent analysis with PEMer workflow on the simulated reads can facilitate parameterize PEMer workflow. BreakDB is a web accessible database developed to store, annotate and dsplay SV breakpoint events identified by PEMer and from other sources.	Structural variation
PERalign	A probabilistic framework is described to predict the alignment to the genome of all paired-end read transcript fragments in a paired-end read dataset. Starting from possible exonic and spliced alignments of all end reads, our method constructs potential splicing paths connecting paired ends. An expectation maximization method assigns likelihood values to all splice junctions and assigns the most probable alignment for each transcript fragment.	RNA-Seq Alignment			C++		Linux
PerM	PerM (Periodic Seed Mapping) uses periodic spaced seeds to significantly improve mapping efficiency for large reference genomes when compared to state-of-the-art programs.	Genomics SNP discovery	Mapping		C++	Apache License 2.0	Linux
Phred	The phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base.		Basecaller		C		Solaris IRIX AIX
Phred Phrap Consed Cross match	The phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base. Phrap is a program for assembling shotgun DNA sequence data. Cross_match is a general purpose utility for comparing any two DNA sequence sets using a 'banded' version of swat. Consed/Autofinish is a tool for viewing, editing, and finishing sequence assemblies created with phrap.		Alignment Assembly Basecaller Smith-Waterman
Phymm	A classifier for metagenomic data, that has been trained on 539 complete, curated genomes and can accurately classify reads as short as 100 base pairs	Metagenomics	Hidden Markov Model
PiCall	Identifies short indel polymorphisms in population sequencing data	InDel discovery Population genetics
PICS	PICS identifies binding event locations by modeling local concentrations of directional reads, and uses DNA fragment length prior information to discriminate closely adjacent binding events via a Bayesian hierarchical t-mixture model.	ChIP-Seq			R
PileLine	PileLine is a flexible command-line toolkit for efficient handling, filtering, and comparison of genomic position (GP) files produced by next-generation sequencing experiments. PileLineGUI adds a graphical interface.		Viewer		Java	LGPL
Pindel	A pattern growth approach to detect break points of large deletions and medium sized insertions from paired end short reads.	InDel discovery Structural variation	Split-read Mapping Localized reassembly/realignment		C++		Linux Mac OS X Windows
Pipeline Pilot	Analysis and workflow development of Next Generation Sequencing and gene expression.	Next Generation Sequencing Gene expression Sequence analysis SNP discovery	General bioinformatics Mapping De-novo assembly Sequence analysis Variant detection Gene expression analysis RNA-Seq analysis ChIP-Seq analysis Genomics Comparative genomics Whole genome resequencing Sequence alignment	Integrated solution wrapping custom and third party tools for integration analysis and reporting	C++ Java Perl R Pilot Script	Commercial	Linux Windows
PIQA	PIQA is a quality analysis pipeline designed to examine genomic reads produced by Next Generation Sequencing technology (Illumina G1 Genome Analyzer). It is a set of libraries for R.		Sequencing Quality Control		R
PoissonSeq	Identify differential expressed genes	Differential Expression
PolyBayesShort	A re-incarnation of the PolyBayes SNP discovery tool developed by Gabor Marth at Washington University. This version is specifically optimized for the analysis of large numbers (millions) of high-throughput next-generation sequencer reads, aligned to whole chromosomes of model organism or mammalian genomes. Developers at Boston College.	SNP discovery					Linux Linux 64
PoolHap	Computational tool for inferring haplotype frequencies from pooled samples when haplotypes are known. In future version, haplotype unknown analysis will be supported.		Mapping Regression.
PoPoolation	Toolbox specifically designed for the population genetic analysis of sequence data from pooled individuals.	Population genetics	Pooled samples		Perl R
PoPoolation2	PoPoolation2 allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences. PoPoolation2 requires next generation sequencing data of pooled genomic DNA (Pool-Seq). It may be used for measuring differentiation between populations, for genome wide association studies and for experimental evolution.	Population genetics Genomics	Pooled samples		Perl R
PRICE	PRICE uses paired-read information to iteratively increase the size of existing contigs.		Assembly		C++
PRINSEQ	PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.	Metagenomics Genomics Metatranscriptomics	Preprocessing Filtering Trimming		Perl	GPLv3	UNIX Mac OS X Windows
ProbeMatch	Matches a large set of oligonucleotide sequences against a genome database using gapped alignments		Mapping				Linux Mac OS X
ProbHD	We present a new strategy for identifying heterozygous sites in a single individual by using a machine learning approach that generates a heterozygosity score for each chromosomal position. Our approach also facilitates the identification of regions with unequal representation of two alleles and other poorly sequenced regions. The availability of confidence scores allows for a principled combination of sequencing results from multiple samples.	Population genetics SNP discovery			Perl R Python
Proxygenes	We introduce a clustering method which significantly reduces the size of a metagenome dataset while maintaining a faithful representation of its functional and taxonomic content.	Metagenomics	Mapping Annotation
Pybedtools	Python extension to BEDTools that allows use of all BEDTools programs directly from Python, as well as feature-by-feature manipulation, automatic handling of temporary files, and more.	Genomics	Mapping	See full description	Python	GPLv2	Windows (Cygwin) Linux Linux 64 Mac OS X
PyroBayes	PyroBayes is a novel base caller for pyrosequences from the 454 Life Sciences sequencing machines.	SNP discovery	Basecaller
PyroMap	PyroMap accurately maps pyrosequencing reads onto reference sequences using a selectively weighted Smith-Waterman (SW^2) algorithm to incorporate quality scores into alignment.		Mapping		Python
PyroNoise	Clustering of pyrosequencing (454) data with noise model (AmpliconNoise) and chimaera removal (Perseus) for sequence diversity analysis.	Phylogenetics Metagenomics
QCALL	SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples	SNP discovery
Qpalma	QPalma is an alignment tool targeted to align spliced reads produced by Next Generation sequencing platforms	RNA-Seq Alignment	Alignment		Python C++
QSeq	QSeq is DNASTAR's Next-Gen application for RNA-Seq,ChIP-Seq, and miRNA alignment and analysis.	ChIP-Seq RNA-Seq MiRNA	Integrated Solution Alignment Visualization Protein Binding Peak Detection			Commercial	Mac OS X 10.6 with Parallels Desktop Windows
QSRA	Quality-value guided Short Read Assembler, created to take advantage of quality-value scores as a further method of dealing with error. Compared to previous published algorithms, our assembler shows significant improvements not only in speed but also in output quality.	De-novo assembly	Assembly
QuadGT	QuadGT is a software package for calling single-nucleotide variants in four sequenced genomes: normal-tumor pairs coupled with parents. Genotypes are inferred using a joint model of parental variant frequencies, de novo germline mutations, and somatic mutations. The model quantifies the descent-by-modification relationships between the unknown genotypes by using a set of parameters in a Bayesian inference setting.	SNP discovery De novo Germline and Somatic mutations	SNP calling Variant Calling		Java
Quake	Program to detect and correct errors in DNA sequencing reads. Using a maximum likelihood approach incorporating quality values and nucleotide specific miscall rates,		Error correction
QUAST	QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Quality Control Genomic Assembly Evaluation Sequence analysis	Assembly QC Visualization Quality Control	Data Visualization Assembly Quality Evaluation Detailed Reports	Python C Perl	GPLv2	Linux Mac OS X
QuEST	QuEST is a Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitations (ChIP-Seq or ChIPseq).	ChIP-Seq			C++	GPLv2
Quip	Aggressive compression of FASTQ and SAM/BAM files.		Data compression		C	BSD (3-clause)	any
R2R	R2R is a simple to use package for very sensitive analysis of short read sequence data obtained by NextGen sequencing techniques. R2R was developed in conjunction with data obtained on the Illumina GA platforms. R2R is written in simple Perl script and runs equally well under MS Windows, Mac OS and Linux/Unix operative systems.	SNP discovery	Alignment		Perl
R453Plus1Toolbox	Facilitates analysis of data from 454 sequencer in R/Bioconductor.				R
RACA	Reference-Assisted Chromosome Assembly (RACA)
RApiD	Tools for processing restriction site associated DNA sequencing.	SNP discovery			Perl C++	GPLv3
RAPSearch	Fast protein similarity search tool for short reads that utilizes a reduced amino acid alphabet and suffix array to detect seeds of flexible length.	Metagenomics	Alignment		C++	GPLv3
Ray	de novo genome assembly is now a challenge because of the overwhelming amount of data produced by sequencers. Ray assembles reads obtained with new sequencing technologies (Illumina, 454, SOLiD) using MPI 2.2 -- a message passing inferface standard.	De-novo assembly	Assembly	* MPI 2.2 * ISO/IEC C++ 2003 * de Bruijn * paralleled * Illumina data	C++	GPL	Linux POSIX
RazerS	RazerS allows the user to align sequencing reads of arbitrary length using either the Hamming distance or the edit distance. The tool can work either lossless or with a user-defined loss rate at higher speeds.	Mapping Read alignment	SWIFT Filter Myers Bitvector Algorithm	Gapped alignment paired-end mapping	C++	GPLv3	UNIX Mac OS X Windows
RDiff	rDiff is an open source tool for accurate detection of differential RNA processing from RNA-Seq data. It implements two statistical tests to detect changes of the RNA processing between two samples. rDiff.parametric is a powerful test, which can be applied for well annotated organisms to detect changes in the relative abundance of isoforms. rDiff.nonparametric is an alternative when the annotation is incomplete or missing.	RNA-Seq Alignment Differential RNA processing regulation Alternative Splicing RNA-Seq Transcriptomics	Statistical testing		Python Matlab	Open Source	Linux Mac OS X
RDP Pyrosequencing Pipeline	The Ribosomal Database Project's Pyrosequencing Pipeline aims to simplify the processing of large 16s rRNA sequence libraries obtained through pyrosequencing. This site processes and converts the data to formats suitable for common ecological and statistical packages such as SPADE, EstimateS, and R.	Metagenomics	Alignment Database submission preparation Format conversion				browser based
Readaligner	A tool for mapping (short) DNA reads into reference sequences.		Mapping
ReadDepth	Detects copy number aberrations in deep sequencing data	Copy number estimation			R	Apache License 2.0
REAL	REad ALigner for Next-Generation sequencing reads		Mapping		C++	GPLv3	Linux
Reaper	Reaper is a program for demultiplexing, trimming and filtering short read sequencing data.	Next Generation Sequencing	Filtering Adapter Removal (software) Trimming Sample Barcoding Sequencing Quality Control QC	Memory efficient and fast.	C	GPL v3	Linux UNIX Mac OS X
Reconciliator	The tool for merging assemblies		Assembly		Perl		Linux
RECOUNT	Probabilistic tag count error correction for next generation sequencing data (Solexa/Illumina).	RNA-Seq Quantitation	Expectation Maximization		C++	GPL	Linux
RefCov	WashU Reference Coverage tool for analyzing the depth, breadth, and topology of sequencing coverage	Copy number estimation
Repitools	Toolbox of procedures to interrogate and visualize epigenomic data. Part of BioConductor	ChIP-Seq ChIP-on-chip	Sequencing Quality Control Visualization Methylation Calling Statistical testing		R	LGPL
Reptile	A new algorithm for short read error correction that harvests information from k-spectrum and read decomposition	Genomics	Sequencing Quality Control		C++	GPL Boost
ReSeqSim	A simulation toolbox that will help us optimize the combination of different technologies to perform comparative genome re-sequencing, especially in reconstructing large structural variants (SVs).	Structural variation	Mapping Simulation
RGA	Reference-guided assembler	SNP discovery	Assembly
RiboPicker	riboPicker is a publicly available tool that is able to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets. riboPicker is available as both standalone and web-based versions.	Metagenomics Genomics Metatranscriptomics	Preprocessing RRNA filtering		Perl C	GPLv3	UNIX Mac OS X
RMAP	Assembles 20 - 64 bp Solexa reads to a FASTA reference genome. By Andrew D. Smith and Zhenyu Xuan at CSHL. (published in BMC Bioinformatics). POSIX OS required.	DNA methylation	Mapping Bisulfite mapping			GPLv3	Linux Mac OS X
RNA	A randomized Numerical Aligner for Accurate alignment of NGS reads	Read alignment	Mapping Hash Table Based	Fast Accurate	C++	GPL v3	Linux UNIX Windows Mac OS X
RNA-MATE	A recursive mapping strategy for high-throughput RNA-sequencing data.	RNA-Seq Alignment RNA-Seq Quantitation	Colorspace
RNASEQR	a streamlined and accurate RNA-seq sequence analysis program	Alternative Splicing	Read mapping
Rnnotator	Automated software pipeline that generates transcript models by de novo assembly of RNA-Seq data without the need for a reference genome	De novo transcriptome assembly				Commercial Freeware
RobiNA	RobiNA is a Java GUI that enables the user to graphically call differentially expressed genes. For read mapping it relies on bowtie and for the differntial expression analysis it builds on an R backbone running DESeq and edgeR.	RNA-Seq	Differentially expressed gene identification	Trimming differential expression graphical display	Java R	GPL	Windows Linux Mac OS X
Rolexa	Allows fast and accurate base calling of Solexa's fluorescence intensity files and the production of informative diagnostic plots.	Sequencing	Basecaller		R
RSAT peak-motifs	A workflow combining a series of time- and memory-efficient motif analysis tools to extract motifs from full-size collections of peaks as generated by ChIP-seq, ChIP-chip or other ChIP-X technologies.	ChIP-Seq Regulatory genomics Epigenomics	Motif discovery Motif scanning Motif comparison		Perl CGI Python C	Commercial Freeware	UNIX Mac OS X Linux
RSEM	We present a generative statistical model and associated inference methods that handle read mapping uncertainty in a principled manner. Through simulations parameterized by real RNASeq data, we show that our method is more accurate than previous methods. Our improved accuracy is the result of handling read mapping uncertainty with a statistical model and the estimation of gene expression levels as the sum of isoform expression levels.	RNA-Seq Alignment RNA-Seq Quantitation			C++
RSEQtools	RSEQtools includes a format specification for RNA-Seq data that provides confidentially-aware; data summaries as well as several tools for performing common analyses: expression measurements (e.g. RPKMs), creation of signal tracks, segmentation, annotation manipulations, etc.	RNA-Seq Quantitation			C	Creative Commons - Attribution; Non-commercial 2.5	Mac OS X UNIX Linux
Rsolid	Rsolid implements a version of the quantile normalization algorithm that transforms the intensity values before calling colors		Colorspace Basecaller		R C
Rsubread	Rsubread is Bioconductor R package, which provides facilities to performing read alignments using the Subread aligner. It also includes other functionalities such as featureCounts read summarization function.	Next-generation sequencing	Read mapping Read summarization Quality assessement		R C	GPL v3	Linux 64 Mac OS X; x86 64 Mac OS X
RTG Investigator	Comprehensive analysis pipelines powered with unique mapping speed and sensitivity deliver deep genomic analysis in variant detection and metagenomic applications with Illumina, Ion Torrent, Complete Genomics and Roche 454 data sets.	Exome and whole genome variant detection Metagenomics SNP discovery InDel discovery	Mapping Alignment Translated nucleotide search K-mer analysis Species frequency estimation Contaminant filtering Read depth analysis			Commercial Freeware	Linux Mac OS X Windows
RUbioSeq	RUbioSeq has been developed to facilitate the primary and secondary analysis of resequencing projects by providing an integrated software suite of parallelized pipelines to detect exome variants (SNVs and CNVs) and to perform Bisulfite-seq analyses automatically. RUbioSeq's variant analysis results have been already validated and published. AVAILABILITY: http://rubioseq.sourceforge.net/	Exome analysis Copy number estimation Bisulfite Sequencing	Somatic variant calling		Perl		UNIX
S-MART	S-MART manages your RNA-Seq and ChIP-Seq data.	RNA-Seq ChIP-Seq			Python Java		Linux Mac OS X Windows
SAMMate	GUI for processing SAM/BAM and BED files. The software allows users to accurately estimate gene expression scores using short reads originating from both exons and exon-exon junctions, to generate wiggle files for visualization in UCSC genome browser, and to generate an alignment statistics report.	RNA-Seq Quantitation	Sequence analysis		Java	GPLv3	Windows Mac OS X
Samscope	Samscope is a lightweight SAM/BAM file viewer that makes visually exploring next generation sequencing data as intuitive as Google Maps. Samscope uses multiple layers to simultaneously (or sequentially) view SAM/BAM related features like coverage or allele frequency, or ChIP-SEQ features like polarity from as many files as you like. The paging-friendly binary file layout makes it feasible to browse data sets far larger than the system's available RAM.	ChIP-Seq RNA-Seq Genomics	Visualization Read mapping SAMtools		C++	AGPL	POSIX Linux
SAMStat	SAMStat is an efficient C program for displaying statistics of large sequence files.		Sequencing Quality Control		C	GPLv3	UNIX
SAMtools	Various utilities for processing alignments in the SAM format, including variant calling and alignment viewing.	SNP discovery	Simulation Programming Library Assembly visualization	Integrated solution API	C	MIT
Savant Genome Browser	Savant is a genome browser which combines visualization of HTS and other genome-based data with powerful analytic tools.	Genomics	Visualization Viewer Alignment viewer	Plugin framework Bookmarking Table View fast memory efficient	Java	Apache License 2.0	Windows Linux all supporting JVM Mac OS X
Scaffolder	Edit your genome sequence using a simple human readable syntax. Manage contig positions and add inserts all in a plain text file.		Scaffolding		Ruby	MIT	Linux Mac OS X
SCALCE	SCALCE (skeɪlz) is fast FASTQ compression utility that utilizes locally consistent parsing for better compression rate. It achieves around 2X more compression than gzip alone.	Genomics	Data compression	FASTQ file compression	C		Linux 64 Linux
SCARF	Scaffolded and Corrected Assembly of Roche 454 (SCARF) is a next-generation sequence assembly tool for evolutionary genomics that is designed especially for assembling 454 EST sequences against high-quality reference sequences from related species.		Assembly			GPLv3
Scripture	Tool for assembling transcriptome from paired-end Illumina RNA-Seq data	RNA-Seq Alignment
SEAL	Read mapper and duplicate remover.		Mapping Hadoop		Python C++ Java	GPLv3
SEECER	Error correction for RNA-Seq data	RNA Seq analysis		supports multicore processors	C
SEED	Tool to cluster sequence reads prior to assembly or other operations.	Metagenomics	Clustering		C++		Mac OS X Linux Windows
Segemehl	Map short reads to known genome with tolerance for mismatches and indels using suffix arrays for high accuracy matching	Genomics	Mapping	fast precise low cost for high-error matching	C C++
Segtor	A software tool to annotate large sets of genomic coordinates, intervals, SNVs, indels and translocations with respect to known genes.	SNP Annotation	Annotation	SNP annotation	Perl C	Non-commercial	Linux Mac OS X
Seq2HLA	seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.	Transcriptomics	Mapping Read alignment HLA typing		Python R		Unix Mac OS X
SeqAn	C++ template library with many sequence analysis algorithms and datastructures.	Sequence analysis Genomics Phylogenetics	Programming Library		C++	BSD (3-clause)	UNIX Mac OS X Windows
SeqBuster	SeqBuster, a web-based bioinformatic tool offering a custom analysis of deep sequencing data at different levels, with special emphasis on the analysis of miRNA variants or isomiRs and the discovering of new small RNAs.	Small RNA transcriptome MiRNA	Mapping Annotation	Annotation and detection of miRNAs and other small RNAs	Java R	Commercial Freeware	Mac OS X Linux
SeqCons	SeqCons is an open source consensus computation program for Linux and Windows. The algorithm can be used for de novo and reference-guided sequence assembly.		Assembly				Linux Windows
SeqEM	Genotype-calling algorithm that estimates parameters underlying the posterior probabilities in an adaptive way rather than arbitrarily specifying them a priori. The algorithm applies the well-known EM algorithm to an appropriate likelihood for a sample of unrelated individuals with next-generation sequence data, leveraging information from the sample to estimate genotype probabilities and the nucleotide-read error rate.	SNP discovery	Expectation Maximization
SeqGSEA	Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing	Biomedical Sciences Genomics RNA-Seq	Statistics Functional analysis Gene set enrichment analysis	integrative analysis	R	GPL (>= 3)	any
SeqMan NGen	Sequence assembly software using traditional, next-gen, and third-gen techonologies. Subsequent analysis of the assembly, including SNP discovery, coverage evaluation and consensus annotation is provided through full integration with Lasergene.	Genomics De-novo assembly De novo transcriptome assembly Whole Genome Resequencing SNP discovery InDel discovery ChIP-Seq RNA-Seq Alignment	Mapping Assembly Alignment Paired End			Commercial	Windows Mac OS X Linux
SeqMap	SeqMap is a tool for mapping large amount of short sequences to the genome.		Mapping	command line parallel execution			Mac OS X Windows Linux
SeqMINER	seqMINER is an integrated portable ChIP-seq data interpretation platform with optimized performances for efficient handling of multiple genomewide datasets. seqMINER allows comparison and integration of multiple ChIP-seq datasets and extraction of qualitative as well as quantitative information. seqMINER can handle the biological complexity of most experimental situations and proposes supervised methods to the user in data categorization according to the analysed features. In addition, through multiple graphical representations, seqMINER allows visualisation and modelling of general as well as specific patterns in a given dataset. Moreover, seqMINER proposes a module to quantitatively analyse correlations and differences between datasets.	ChIP-Seq			Java	GPLv3	platform-independent
SeqMonk	A tool to visualise and analyse high throughput mapped sequence data	Genomics Epigenomics	Visualization Assembly visualization Statistical testing Alignment viewer	Genome Viewer Data Visualisation Data Quantitation filtering and analysis	Java	GPLv3	Windows Mac OS X Linux
SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Genomics De-novo assembly		Merges overlapping paired-end reads strips adapters off of reads.	C	MIT	POSIX
SeqSaw	A package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data.	RNA-Seq Alternative Splicing	Mapping Alignment	Short Spliced Sequence Mapping Tool	C++	GPL	Linux
SeqSeg	An algorithm to identify chromosomal breakpoints using massively parallel sequence data	Copy number estimation			Matlab
SeqSite	SeqSite is an efficient and easy-to-use software tool implementing a novel method for identifying and pinpointing transcription factor binding sites. It first detects transcription factor binding regions by clustering tags and statistical hypothesis testing, and locates every binding site in detected binding regions by modeling the tag profiles. It can pinpoint closely spaced adjacent binding sites from ChIP-seq data. This software is coded in C/C++, and supports major computer platforms.	ChIP-Seq Functional Genomics Regulatory element annotation	ChIP-Seq Peak calling Statistical Modelling Statistical testing	stand-along software tool can run on major computer platforms	C C++	GPL	Linux Mac OS X Windows
SeqSolve	Simple analysis of Next Generation Sequencing data.	RNA-Seq ChIP-Seq Transcriptomics MiRNA NcRNAs SRNA Differential Expression Alternative Splicing New gene discovery Quality Control	SAMtools Cufflinks IGV MACS Tibco Spotfire	User-friendly Scientifically relevant Reliable Scalable		Commercial	Windows Linux
SeqTrim	A pipeline for preprocessing sequences.		Trimming
Sequedex	Sequedex classifies short reads for phylogeny and function at high speed	Metagenomics Phylogenetics Transcriptomics genetics	Sequence analysis Signature methods	Fast protein fragments identified	Java Python	Commercial Freeware	Linux 64 Mac OS X
SequenceVariantAnalyzer	DNA sequence information underpins genetic research, enabling discoversies of important biological or medical benefit. Compared with previous discovery strategies, a whole-genome sequencing study is no longer constrained by differing patterns of linkage disequilibrium, thus, in theory, is more possible to directly identify the gentic variants contributing to biological traits or medical outcomes. The rapidly evolving high-throughput DNA sequencing technologies have now allowed the fast generation of large amount of sequence data for the purpose of performing such whole-genome sequencing studies, at a reasonable cost. SequenceVariantAnalyzer, or SVA, is a software tool that we have been developing to analyze the genetic variants identified from such studies. URL: http://www.svaproject.org/	Personal genomics Genomics Sequence analysis	Annotation Genetic variation annotation Genome browser	Variant annotation and analysis	Java		Linux 64
Sequencher	Desktop alignment software now with plugins to MAQ and GSNAP for NGS sequence date	De-novo assembly SNP discovery	Assembly Alignment	Bisulfite sequencing consensus sequence generation and export SNP/InDel/Read Error display and search		Commercial	Windows Mac OS X
SeqWare	SeqWare provides tools designed to support massively parallel sequencing technologies.		LIMS Workflow		Java	GPLv3	Linux
SeqWords	SeqWords is a featherweight object for the calculation of n-mer word occurrences in a single sequence.		K-mer analysis	Part of BioPerl	Perl	Perl artistic licence
SESAME	Gnotyping of multiplexed individuals for several markers based on NGS amplicon sequencing.	Genotyping Targeted resequencing				GPLv3	Windows Linux
SEWAL	Processing of deep sequencing data from in vitro selection experiments	In vitro selection
Sff2fastq	The program 'sff2fastq' extracts read information from a SFF file, produced by the 454 genome sequencer, and outputs the sequences and quality scores in a FASTQ format.		Conversion				Linux
SGA	SGA is a de novo assembler designed to assemble large genomes from high coverage short read data.		Assembly		C++	GPLv3	Linux
SHARCGS	SHARCGS is a suitable tool for fully exploiting novel sequencing technologies by assembling sequence contigs de novo with high confidence and by outperforming existing assembly algorithms in terms of speed and accuracy.	De-novo assembly	Assembly		Perl		Linux
SHE-RA	The SHE-RA software turns error-prone short reads into Sanger-quality composite reads.		Error correction			Open Source
Sherman	bisulfite-treated Read FastQ Simulator	Genomics Bisulfite Sequencing DNA methylation	Simulation		Perl	GPLv3	Linux Mac OS X
ShoRAH	Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.	Metagenomics	Haplotype reconstruction Mapping			GPLv3	Linux Mac OS X
Shore	Analysis suite for short read data.	Structural variation SNP discovery	Mapping				Linux Mac OS X POSIX
… further results