Software

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Stubs:
App. Article Size Article 'Score'
HMMSplicer 172 20
Reconciliator 199 40
MAQGene 210 20
CHiPSeq 211 30
RACA 218 0
Fuzzypath 219 40
Arf 227 0
BreakSeq 230 20
CPTRA 230 20
ChIPseqR 232 20
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  Bioinformatics method Biological technology Operating system Language Maintained Licence
.NET BIO Windows
Linux
C# Yes
4peaks Sequence analysis Sanger Mac OS X Yes Freeware
A5 Sequence assembly Illumina Linux
Mac OS X
Yes GPLv3
AB Large Indel Tool Mapping ABI SOLiD Linux 64 Perl No GPL
AB Small Indel Tool Read mapping
Sequence alignment
ABI SOLiD Linux 64 Perl
C++
Maybe GPL
ABBA Sequence assembly
Scaffolding
Linux Maybe Artistic License
ABMapper Read mapping
Sequence alignment
Illumina Linux C++
Perl
Yes GPLv3
ABySS Sequence assembly
Sequence assembly (de-novo assembly)
Illumina
454
ABI SOLiD
Sanger
POSIX
Linux
Mac OS X
C++ Yes Commercial
Freeware
Adapter Removal (software) Adapter removal Illumina
454
Linux 64
Windows
Mac OS X
Java Yes Custom Licence
ADTEx Statistical calculation Illumina GNU/Linux Python
R
Yes GPLv3
AGE Sequence alignment Illumina Maybe Creative Commons license (Attribution-NonCommerical).
AGILE Mapping 454 C Yes
Agp2amos Formatting Windows
Linux
Maybe
Alcovna Java Maybe
ALEXA-Seq Perl Maybe GPLv3
ALLPATHS Sequence assembly
Sequence assembly (de-novo assembly)
Yes
Alta-Cyclic Base-calling Illumina No
AMOS Sequence assembly
Sequence assembly validation
Formatting
Integrated solution
Sequence assembly visualisation
Linux C
Perl
Maybe
ANCHOR Sequence assembly
Sequence assembly validation
Illumina Linux C++
Python
Yes BCCA (academic use)
AnCorr Correlation
Statistical calculation
Any Cross-Platform Perl
C
CGI
PHP
JavaScript
Yes free for non-commercial academic research
Anno-J Visualisation No Creative Commons - Attribution-NonCommercial-ShareAlike
ANNOVAR Annotation
Variant prioritisation
Linux
Windows
Mac OS X
Perl Yes Commercial
Freeware
Arachne Sequence assembly Sanger Maybe
AREM Peak calling
Read mapping
Illumina Linux Python Yes
Arf Maybe
Array Suite (Array Studio/Server) Read mapping
Gene expression profiling
454
Illumina
Windows C# Yes Commercial
ArrayExpressHTS R Maybe
ArrayStar Differential expression analysis
Ontology comparison
Genetic variation analysis
Statistical calculation
Affymetrix
Roche NimbleGen
Agilent
GenePix
Illumina
Windows 7 64-bit or Higher
Mac OS X 10.7
10.8
or 10.9 with Parallels Desktop
Yes Commercial
ASC Statistical calculation and probability Maybe
ATAC Sequence assembly validation
Sequence alignment
Linux Maybe
Atlas Suite Variant calling Illumina
454
ABI SOLiD
POSIX Ruby
C
Yes BSD
Atlas-SNP2 UNIX Ruby Yes Freeware
Avadis NGS Sequence alignment
Sequencing quality control
Sequence analysis
Visualisation
Analysis
Illumina
454
ABI SOLiD
Ion Torrent
PacBio
Ion proton
Windows
Linux
Mac OS X
Java
R
Yes Commercial
Baa.pl Sequence alignment analysis
Sequence assembly validation
Any any Perl Yes GPL
Bambino Java Maybe
Bambus Scaffolding Yes
BAMseek Sequence alignment visualisation Any Cross-Platform Java Yes GPLv3
BamTools Sequence alignment analysis Cross-Platform C++ Yes MIT
BamView Visualisation Mac OS X
UNIX
Windows
Java Maybe GPL
Barcode generator DNA barcoding Illumina Python Maybe
Barcrawl Bartab DNA barcoding 454 Maybe GPL
BarraCUDA Read mapping
Sequence alignment
Illumina
ABI SOLiD
Linux C
C++
CUDA
Yes GPLv3
MIT
Batman Java No LGPL
BayesCall Base-calling Illumina C++
Python
No GPLv3
BayesPeak Statistical calculation Illumina R Yes GPL
BaySeq Differential expression analysis Illumina R Yes
BBMap Read mapping
RNA-Seq analysis
Sequence alignment
Sequence trimming
Sequence contamination filtering
Sanger
Illumina
454
Ion Torrent
PacBio
Windows
*NIX
Mac OS X
all supporting JVM
Java 7 Yes BSD
BBSeq R Maybe
Bcbio-nextgen Sequencing quality control
Filtering
Sequence trimming
Read mapping
Peak calling
Differential expression analysis
Genomic region matching
Sequence alignment
Genotyping
Sequence motif recognition
platform-independent Python Yes MIT
BEADS Standardisation and normalisation Illumina Maybe
BEAP Read mapping Maybe
BEDTools Mapping Linux
Mac OS X
C++ Yes GPLv2
Bedutils Maybe
Belvu Sequence alignment visualisation Linux Maybe
BFAST Read mapping
Sequence alignment
Genome indexing
ABI SOLiD
Helicos
454
Illumina
Solaris
UNIX
C Yes GPL
BFCounter K-mer counting C++ Yes GPLv3
BigBWA Read mapping
Mapping
Sequence alignment
Illumina
ABI SOLiD
SOLiD
Ion Torrent
Ion proton
Linux 64 Java Yes GPLv3
BING Base-calling
Sequencing quality control
Illumina Maybe
BioJava Java Yes LGPL 2.1
Bionimbus Linux
Amazon EC2
cloud
Yes
BioNumerics Sequence assembly
Read mapping
Annotation
Variant calling
Comparative genomics
Analysis pipeline
Sequence alignment
Genome visualisation
Sanger
Illumina
Ion Torrent
PacBio
Windows 7 or Higher Yes Commercial
BioPerl Cross-Platform Perl Yes
BioPHP PHP Yes GPLv2
Biopieces Sequence alignment
Sequencing quality control
Sequence analysis
Visualisation
Perl
Python
Ruby
C
Yes GPLv2
Biopython Sequence parsing Linux
Windows
Mac OS X
Python Yes Biopython License (MIT/BSD style)
BioRuby Cross-Platform Ruby Yes
BioSmalltalk Sequence parsing Linux
Windows
Mac OS X
Smalltalk Yes
BiQ Analyzer Windows
Linux
Mac OS X
Solaris
Java Yes
BiQ Analyzer HT Windows
Linux
Mac OS X
Solaris
Java Yes
Bis-SNP SNP calling
Bisulfite mapping
Methylation calling
Illumina Linux
Mac OS X
Java
Perl
Yes MIT
Bismark Bisulfite mapping
Read mapping
Methylation calling
Linux
Mac OS X
Windows
Perl Yes GPLv3
Bison Bisulfite mapping
Read mapping
Methylation calling
Unix-like
Linux
Mac OS X
C Yes
BLAST Linux Yes
BLAST Ring Image Generator Visualisation
Sequence assembly visualisation
Cross-Platform Yes
BLAT Read mapping
Sequence alignment
Linux
Mac OS X
C Maybe Freeware
Blixem Sequence alignment visualisation Linux Maybe GPL
BOAT Read mapping Maybe GPL
Bort Any any Perl Yes
BOW Maybe
Bowtie Read mapping
Genome indexing (Burrows-Wheeler)
Mac OS X
Linux
Windows
Yes
BRAT Bisulfite mapping
Mapping
Illumina Maybe GPLv3
BRCA-diagnostic Perl Maybe
BreakDancer Perl
C++
Maybe GPLv3
Breakpointer Statistical calculation C++
Perl
Yes GPL
BreakSeq Read mapping Maybe
BreakTrans Post-analysis Maybe
Breakway Sequence analysis
SNP calling
ABI SOLiD
Illumina
454
Sanger
Linux
Mac OS X
Windows
Perl Yes GPL
BS Seeker Bisulfite mapping Python Maybe
BS-Seq Bisulfite mapping Maybe
BSMAP Read mapping
Bisulfite mapping
Linux 64 C++ Maybe GPLv3
BSSim Modelling and simulation Illumina
454
ABI SOLiD
UNIX
Linux
Mac OS X
Windows
Python Yes GPLv3
Btrim Sequence trimming Linux Yes
BWA Read mapping Sanger
Illumina
454
ABI SOLiD
UNIX C Yes GPLv3
MIT
BWA-SW Read mapping Sanger
Illumina
454
UNIX C Yes GPLv3
MIT
CABOG Sequence assembly Sanger
454
Illumina
Linux Yes
CANGS Primer removal
Sequence trimming
Sequencing quality control
454 Yes
CARPET Genotyping C++ No
CASHX Read mapping Maybe
CATCH Clustering
Sequence alignment
Java Yes Open Source
CatchAll Yes
CEQer Any Windows
Mac
Linux
C# Yes GPLv3
CexoR Peak calling Illumina HiSeq
454
ABI SOLiD
Ion Torrent
Illumina Solexa
Illumina
Linux
Mac OS X
Windows
R Yes GPL-2 + file LICENSE
CGA Tools File reformatting Complete Genomics Linux
UNIX
Mac OS X
C++ Yes Apache License 2.0
CHiCAGO Peak calling Any Linux
OSX
R
Python
Yes Artistic-2.0
ChimeraScan Maybe
ChIP-Seq (application) Peak calling
Read mapping
Illumina Linux
Mac OS X
C
Perl
Yes GPL
ChIPmeta Peak calling Maybe
ChIPMunk Sequence motif comparison
Sequence motif discovery
platform-independent Java Yes Freeware
CHiPSeq Peak calling Maybe
ChIPseqR R Maybe
Chipster Sequencing quality control
Sequence trimming
Read mapping
Peak calling
Sequence motif recognition
Differential expression analysis
Pathway or network analysis
Methylation analysis
Genome visualisation
platform-independent Java
R
Yes GPLv3
ChromaSig Sequence motif recognition Perl
C
Maybe
ChromHMM Statistical calculation Java Yes GPLv3
Circos Visualisation Windows
Linux
Perl Yes
CisGenome Gibbs sampling
Integrated solution
Sequence motif recognition
Data retrieval
UNIX
Windows
C
C++
Yes
Cistrome Python Yes
CLCbio Genomics Workbench Read mapping
Sequence assembly
Sequence alignment
Ab-initio gene prediction
Adapter removal
Annotation
Bisulfite mapping
SNP calling
Sequence assembly (de-novo assembly)
Heat map generation
Sequence assembly validation
454
Illumina
ABI SOLiD
Helicos
Sanger
Ion Torrent
Windows
Mac OS X
Linux
Java
C++
Yes Commercial
Clean reads Sequence trimming
Sequencing quality control
Python Maybe
CleaveLand Perl
R
Yes Freeware
CLEVER Any
Illumina
any C++
Python
Yes GPLv3
ClipCrop Maybe
CloudAligner Read mapping
Hadoop
cloud Java Maybe GPL
CloudBurst Read mapping Java No
ClustDB Linux Maybe
Cluster Flow Analysis pipeline Linux Perl Yes GPLv3
CNANorm Peak calling
Standardisation and normalisation
Illumina Linux
Mac OS X
Windows
R
Perl
Yes GPLv2
CNAseg Maybe
CNAseg Maybe
CNB MetaGenomics tools 454
Illumina
Linux
Unix-like
POSIX
Bash
Perl
Python
C
Yes EU-GPL
CnD D Maybe GPL
CNVer Perl
C++
Yes
CnvHMM Illumina Linux No
CNVkit Variant calling Illumina GNU/Linux
Mac OS X
Python Yes BSD
CNVnator Maybe
CNVseq Perl
R
Maybe
CompreheNGSive Visualisation Mac OS X
Linux
Python
Qt
Yes LGPL
CoNAn-SNV C Maybe
ConDeTri Sequence trimming Illumina Perl Yes
ContEst Sequencing quality control Java Maybe BSD
Contra Illumina Linux 64
Linux
Python
R
Yes GPLv3
Contrail Sequence assembly
Sequence assembly (de-novo assembly)
Hadoop
Yes
CopySeq Illumina Mac OS X
Linux
Java
R
Yes
Coral Sequence error correction C++ Yes
CORAL (Contig Ordering Algorithm) Sequence error correction Java Maybe
Cortex Sequence assembly
Variant calling
C Yes GPLv3
CPTRA Python Maybe
CPTRA Python Maybe
CRAC Read mapping
Genome indexing (Burrows-Wheeler)
Illumina
454
Ion Torrent
Linux
Linux 64
Mac OS X
C++ Yes CeCILL
CRAVAT Annotation
Variant prioritisation
Sequence annotation
SNP annotation
Variant classification
Web
Linux
Yes
CRISP Python Maybe
Crossbow Read mapping Yes
Crossbow Read mapping Yes
CUDA-EC Sequencing quality control C Maybe
Cufflinks Transcriptome assembly
Read mapping
Differential expression analysis
Illumina
454
Ion Torrent
Illumina HiSeq
Illumina Solexa
Yes Boost
CummeRbund Visualisation Illumina Maybe
Curtain Sequence assembly
Sequence assembly (de-novo assembly)
Illumina
454
ABI SOLiD
Maybe Apache License 2.0
Cutadapt Python
Cython
Yes MIT
DCLIP Sequence alignment analysis NGS UNIX
Unix-like
Perl
C
Yes
DecGPU Sequence error correction Linux C++ Yes GPLv3
DeconSeq Sequence contamination filtering Sanger
454
Ion Torrent
PacBio
UNIX
Mac OS X
Perl
C
Yes GPLv3
DeepTools Standardisation and normalisation
Visualisation
Conversion
Illumina HiSeq
454
Illumina
Linux
Mac OS X
Python Yes GPLv3
DeFuse Yes
DEGseq Differentially expressed gene identification R Yes
DESeq Statistical testing
Sequencing quality control
UNIX
Windows
Mac OS X
R Yes GPLv3
DIAL Linux C
Python
Maybe MIT
DiBayes Maybe GPL
DiffBind Differential binding sites Illumina
ABI SOLiD
454
Any
Illumina HiSeq
Illumina Solexa
Linux
Mac OS X
Windows
R Yes Artistic-2.0
Diffreps Differential Binding Illumina
ABI SOLiD
Linux
Windows
Mac OS X
Perl Yes GPLv3
Dindel Localised reassembly Illumina Maybe
DiscoSnp Sequence assembly (de-novo assembly)
Read depth analysis
All Unix-like
iOS
C++ Yes CeCILL
DNA Baser Sequence assembly
Sequence assembly editing
Sequence analysis
Sanger
454
Windows Yes Commercial
Freeware
DNA Chromatogram Explorer Chromatogram visualisation
File reformatting
Sanger Windows Yes Freeware
DNAA Statistical calculation
Sequencing quality control
Modelling and simulation
ABI SOLiD
Illumina
454
Maybe GPL
DNaseR Nucleic acid sequence feature detection
Peak calling
Illumina HiSeq
454
ABI SOLiD
Ion Torrent
Illumina Solexa
Illumina
Linux
Mac OS X
Windows
R Yes GPL-2 + file LICENSE
DNAzip File reformatting C++ Maybe
DrFAST ABI SOLiD Maybe
DSAP browser based Maybe
DSGseq RNA-Seq analysis
Differential expression analysis
Statistical calculation
Illumina
454
ABI SOLiD
Ion Torrent
Linux
Windows
Mac OS X
C
R
Yes Commercial
Freeware
DSRC File reformatting Maybe
E-miR Illumina Maybe
Ea-utils Sequence trimming
Sequencing quality control
C++ Yes MIT
EagleView Sequence assembly visualisation Maybe
EagleView genome viewer Plotting and rendering Linux
Windows
Mac OS X
No
Easyfig Comparative genomics Any Windows
Mac OS X
GNU/Linux
Python Yes GPLv3
EBCall Maybe
ECHO Sequence error correction Python
C++
Maybe BSD
EDENA Sequence assembly Maybe
EdgeR Statistical calculation Illumina
ABI SOLiD
454
Any
Windows
Mac OS X
UNIX
R Yes LGPL
ELAND Sequence alignment Maybe Commercial
EMBF Mapping Maybe
Epigenome Bisulfite mapping R
Python
Yes
EpiGRAPH Statistical calculation browser based Yes
ERANGE Python Yes
ERDS Maybe
ERGO Genome Analysis and Discovery System SNP annotation
SNP detection
Sequence alignment
Pathway or network analysis
Gene expression analysis
Sequence annotation
Sequence functional annotation
Metabolic network modelling
Sanger
Illumina
454
ABI SOLiD
Ion Torrent
Web Yes Commercial
ERNE Read mapping
Bisulfite mapping
Illumina Linux
Mac OS X
Windows
C++ Yes GPLv3
Error Correction Evaluation Toolkit Sequencing quality control Illumina
454
Ion Torrent
POSIX Python
Perl
Maybe
Est2assembly Sequence assembly Sanger
454
Maybe
ESTcalc Perl Maybe
EULER Sequence assembly
Sequence assembly (de-novo assembly)
Linux C++
Perl
Maybe
ExomeCNV R Maybe
ExomeCopy Linux
Windows
Mac OS X
R Yes GPL 2.0+
ExomePicks Maybe
Exonerate Sequence alignment Any Linux C Yes GPL
FAAST Read mapping 454 Linux Maybe
FaBox all Maybe
FACS Any Linux Perl
f
Yes GPLv2
Falcon Sequence assembly PacBio Yes
FAST: Fast Analysis of Sequences Toolbox Sequence analysis
Sequence parsing
GNU/Linux
Mac OS X
Yes
FastQ Screen Read mapping
Sequencing quality control
Illumina
ABI SOLiD
Linux
Mac OS X
Windows
Perl Yes GPLv3
FastQC Sequencing quality control Illumina
ABI SOLiD
UNIX
Windows
Java Yes GPLv3
FastQValidator Sequencing quality control C++ Maybe
FDM Yes
FeatureCounts Read summarisation Illumina
454
ABI SOLiD
Ion Torrent
Linux 64
Mac OS X
Mac OS X; x86 64
R
C
Yes GPLv3
FHiTINGS Sequence alignment Cross-Platform Python Yes
Figaro K-mer counting Sanger UNIX C++
Perl
Maybe Artistic License
Figaro K-mer counting Sanger UNIX C++
Perl
Maybe Artistic License
Filter Sequence contamination filtering Illumina
454
Linux 64
Windows
Mac OS X
Java Yes Custom Licence
FindPeaks 3.1 Peak calling Illumina Yes GPLv3
FindPeaks 4.0 (Vancouver Short Read Package) Peak calling
Formatting
Sequence alignment analysis
Linux
Windows
Mac OS X
Java Yes GPL
FLASH Sequence assembly
Read pre-processing
Linux 64 C Maybe Open Source
Flexbar Read pre-processing
DNA barcoding
Adapter removal
Sequence trimming
Quality control
Illumina
454
ABI SOLiD
Linux
Windows
Mac OS X
C++ Yes GPLv3
Flower Ion Torrent
454
Haskell Maybe
FlowSim Sequence error correction
Modelling and simulation
454 Haskell Maybe
Flux Modelling and simulation Maybe
Forge Sequence assembly Yes
FragGeneScan C
Perl
Maybe GPL
FrameDP Maybe
FreClu Read mapping Maybe
Freebayes Yes MIT
FREEC Linux
Linux 64
Windows
Maybe
FusionAnalyser Illumina Windows
Linux
C# Yes GPLv3
FusionCatcher Sequence alignment Illumina HiSeq/NextSeq/MiSeq/Solexa *NIX Python Yes GPLv3
FusionHunter Linux
Linux 64
Perl
C
Maybe
FusionMap Split-read mapping Windows
Linux
Linux 64
C# Yes Commercial
Freeware
FusionSeq Sequence alignment analysis Any Mac OS X
UNIX
Linux
C Yes Creative Commons - Attribution; Non-commercial 2.5
Fuzzypath Sequence assembly (de-novo assembly)
Sequence assembly
Maybe
G-Mo.R-Seq Linux Yes CeCILL
G-SQZ File reformatting C++ Maybe
Galaxy Sequence alignment
Sequence assembly
Sequencing quality control
Visualisation
Cross-Platform Python Yes
Galign Read mapping Illumina Maybe GPL
Gambit Visualisation Yes GPL 2.0+
Commercial
GAMES SNP detection
SNP annotation
Indel detection
Illumina Linux Perl Maybe
GASSST Sequence alignment
Mapping
Linux C++ Yes CeCILL
GASV Yes GPLv3
GATK Statistical calculation
Localised reassembly
Java
Python
Yes
GBrowse Visualisation Any Linux
Mac OS X
Windows
Perl Yes Open Source
GeeFu Sequence assembly Ruby Maybe
GEM Peak calling
Sequence motif discovery
Illumina HiSeq
Illumina Solexa
Cross-Platform Java Yes Commercial
Freeware
GEM library Read mapping C
Python
OCaml
No GPLv3
GENALICE MAP Read mapping
Variant calling
Illumina HiSeq X Ten Linux Yes Commercial
GENE-Counter Linux
Mac OS X
Yes
Genedata Expressionist Sequence alignment
Annotation
Bisulfite mapping
Clustering
Gene expression analysis
Genome visualisation
Read mapping
Sequencing quality control
RNA-Seq analysis
Sequence analysis
Statistical calculation
Any Windows
Linux
Java Yes Commercial
Geneious Sequence alignment
Sequence assembly
Sequence assembly validation
Annotation
Genome visualisation
DNA barcoding
Read mapping
Visualisation
Sequence motif discovery
Variant calling
Sanger
Illumina
ABI SOLiD
454
Windows
Mac OS X
Linux
Solaris
Java Yes Commercial
GeneProf Read mapping
Visualisation
Peak calling
Differential expression analysis
Sequencing quality control
Illumina
Illumina HiSeq
Illumina Solexa
browser based Java
JavaScript
Yes Commercial
Freeware
GeneTalk Variant calling
Genetic variation analysis
Sequence contamination filtering
Annotation
Exome analysis
Sequence analysis
Variant classification
Plotting and rendering
Ruby
JavaScript
Yes Freemium
Genomatix Mining Station (GMS) Sequence assembly
Read mapping
SNP calling
Correlation
Illumina
ABI SOLiD
Helicos
454
Windows
Mac OS X
Linux
C++
Java
Flash
Yes Commercial
Genome Trax Illumina
454
ABI SOLiD
Yes Commercial
GenomeBrowse Sequence alignment visualisation
Sequence assembly visualisation
Visualisation
Illumina
ABI SOLiD
Sanger
454
Ion Torrent
Windows
Linux
Mac OS X
Yes
Genomedata Signal Any Linux
Mac OS X
Python
C
Yes GPL
GenomeJack Visualisation Sanger
Illumina
454
ABI SOLiD
Windows
Mac OS X
Linux
Java Yes Freeware
GenomeMapper Sequence alignment
Read mapping
Maybe
Genometa Read mapping
Visualisation
Any Linux
Mac OS X
Windows
Java Yes
GenomeTools POSIX
Linux
Mac OS X
OpenBSD
Windows (Cygwin)
UNIX
C Yes BSD
GenomeView Visualisation
Sequence alignment visualisation
Plotting and rendering
Genome visualisation
Data retrieval
Any platform-independent Java Yes GPL
GenomicTools Genome comparison
Peak calling
Heat map generation
C
C++
Yes GPLv2
GenoMiner Sequence assembly
Plotting and rendering
Sequence error correction
Mutation detection
Peak calling
Gene expression profiling
Sequence alignment
Any Linux Java Yes Commercial
GenoREAD Read mapping
Sequence assembly
Sequence alignment
Sanger Linux 64 Perl
PHP
JavaScript
Yes
GenoViewer Viewer Any platform-independent Java Maybe Freeware
GensearchNGS Sequence alignment
Sequence alignment visualisation
Read alignment
Variant prioritisation
Mutation detection
454
Illumina
Ion Torrent
UNIX
Windows
Java Yes Commercial
GenVision Visualisation Windows
Mac OS X
Yes Commercial
Geoseq Read mapping Yes
GigaBayes SNP calling No
GimmeMotifs Sequence motif comparison Any Linux Python Yes MIT
Girafe Sequence alignment R Maybe
Gk arrays Sequence assembly
Sequence error correction
Read mapping
Illumina
454
Sanger
Linux
Linux 64
Mac OS X
any
C++ Yes CeCILL-C license
GlobalSeq Omnibus test
Global test
Joint significance test
cross-platform R Yes GPL-3
GMAP Sequence alignment
Read mapping
UNIX C
Bourne shell
Yes
Gnumap Read mapping Illumina C++ Yes
Goby framework File reformatting Illumina
ABI SOLiD
454
Java Yes GPLv2
Golden Helix Sequencing quality control
Statistical calculation
Genome visualisation
Annotation
Sequence contamination filtering
Collapsing methods
Variant classification
Variant calling
Illumina
Ion Torrent
Affymetrix
Complete Genomics
Sanger
Agilent
Roche NimbleGen
ABI SOLiD
Windows
Linux
Mac OS X
Yes
Goseq Gene set testing Illumina
ABI SOLiD
UNIX
Windows
R Yes LGPL
Gowinda Functional enrichment
Ontology comparison
Genome-wide association study
Mac OS X
Linux
Windows
Java Yes Mozilla Public License
GPS Peak calling Cross-Platform Java Yes Commercial
Freeware
GPSeq R
C
Maybe
GRIDSS Sequence assembly
Whole genome breakpoint assembly
Split-read mapping
Read alignment
Illumina Cross-Platform Java Yes GPLv3
GRS File reformatting Linux
Linux 64
C
Bourne shell
Maybe Commercial
Freeware
GSNAP Read mapping
Bisulfite mapping
C
Perl
Maybe
Hairpin Annotation Illumina
454
Linux 64
Windows
Mac OS X
Java Yes Custom Licence
Haplowser Visualisation
Haplotype inference
Any Java No GPL
HawkEye Sequence assembly visualisation Linux
Mac OS X
C++ Yes Artistic License
HeliSphere Mapping Helicos Linux Yes Freeware
HI Haplotype reconstruction Illumina Java No
Hicup Read mapping Illumina
Ion Torrent
UNIX
Linux
Mac OS X
Perl Yes GPLv3
HINT Nucleic acid sequence feature detection
Peak calling
all Unix-like Python Yes GPLv3
HiPipe Read mapping
Variant calling
Analysis pipeline
Sanger
Illumina
454
ABI SOLiD
Ion Torrent
platform-independent JavaScript
Java
Bash
Yes
HiTEC Sequence error correction Illumina Linux C++ Yes GPLv3
HMMSplicer Python Maybe
HPeak Maybe
HTSeq Python Yes GPLv3
Hybrid-SHREC Sequence error correction Illumina
454
ABI SOLiD
Java Maybe
IBD2 R
Java
Maybe
Ibis Base-calling Linux
Windows (Cygwin)
Python
C
C++
Yes Non-commercial
ICORN Sequence assembly
Sequencing quality control
Maybe
IDBA Sequence assembly Illumina POSIX
Linux
Linux 64
Maybe
IGV Visualisation Windows
Mac OS X
Linux
Java Yes LGPL
Illuminate Sequencing quality control Illumina
Illumina HiSeq
Unix-like Python Yes MIT
Illuminator Illumina Yes
IMAGE Sequence assembly editing Illumina No
Inchworm Illumina Maybe
InGAP Read mapping
Sequence assembly visualisation
Maybe
Ingenuity Variant Analysis Variant classification Any Maybe
Integrated Genome Browser Visualisation Sanger
Illumina
Affymetrix
454
platform-independent Java Yes Open Source
Iobio Visualisation Any Yes
IOmics Sequence alignment
Sequence assembly
Ab-initio gene prediction
MiRNA analysis
Variant calling
Exome analysis
Illumina cloud Yes Commercial
IQSeq C++ Maybe
ISAAC Linux 64 C++ Yes
Isas Sequence alignment Linux Yes
IsoEM Expectation Maximisation Java Maybe
ISSAKE Sequence assembly Illumina Perl
Python
No GPLv2
JBrowse Visualisation browser based Perl
JavaScript
Yes Open Source
Jellyfish Linux 64
Mac OS X
C++ Maybe GPLv3
JointSLM R Maybe
KARMA Read mapping ABI SOLiD
454
Illumina
Maybe
KBASE Annotation Linux Yes
Kismeth Bisulfite mapping Maybe
Kissnp Sequence assembly
Sequence assembly (de-novo assembly)
Data retrieval
Illumina
454
Linux C Yes CeCILL
Kmergenie Sequence assembly Illumina C++
Python
R
Yes
KNIME Workflows Windows
Mac OS X
Linux
Maybe GPLv3
Knime4Bio Data retrieval any Java Yes GPLv3
Krona Visualisation Linux
UNIX
Mac OS X
JavaScript
Perl
Yes
Lab7 Workflows Any Mac OS X
Linux
Python
JavaScript
Yes Commercial
Lasergene Sequence alignment
Sequence alignment analysis
Annotation
Sequence assembly
Chromatogram visualisation
Sequence analysis
Read mapping
PCR primer design
Scaffolding
Peak calling
454
Sanger
Windows XP
Windows 7 or Higher
Mac OS X 10.7
10
8
or 10.9
Yes Commercial
LAST Sequence alignment C++ Yes GPLv3
LASTZ Read mapping
Sequence alignment
Mac OS X
Linux
Maybe
LobSTR Repeat sequence organisation analysis Illumina UNIX C++
R
Python
Yes Freeware
LOCAS Sequence assembly Linux C++ Maybe
LookSeq Sequence assembly visualisation Maybe
LSKB, Life Science Knowledge Bank Analysis pipeline
Annotation
SNP calling
Classification
Pathway or network analysis
Sequence analysis
Functional analysis
Differential expression analysis
Yes
MACS Peak calling platform-independent Python Yes Artistic License
MagicViewer Visualisation
SNP calling
Illumina platform-independent Java Yes
MapDamage Sequencing quality control
Statistical calculation
Illumina Linux
Mac OS X
Python
R
Yes
MapNext Sequence alignment C++
Perl
Maybe
Mapsembler Sequence assembly
Read mapping
Illumina
454
Linux C Yes CeCILL
MapSplice Mapping Linux C++
Python
Yes
MapView Visualisation Linux
Windows
No
MAQ Read mapping C++
Perl
No GPL
MAQGene Read mapping
Integrated solution
Maybe
MARGARITA Maybe
Mason Modelling and simulation
Sequence assembly
Mapping
Illumina
454
Sanger
UNIX
Windows
C++ Yes GPLv3
Mauve Sequence alignment comparison
Visualisation
Sequence assembly validation
Any Mac OS X
Windows
Linux
C++
Java
Yes GPL
MAXIMUS Sequence assembly Any Yes
MAYDAY Visualisation Maybe
Meerkat Illumina Maybe
MEGAN Maybe Commercial
Freeware
Megraft Sequence analysis 454
ABI SOLiD
Illumina
Ion Torrent
Sanger
Linux
UNIX
Mac OS X
Perl Yes GPLv3
Meraculous Sequence assembly Perl
C
Maybe
METAGENassist Visualisation
Statistical calculation
Sequence clustering
Yes
[email protected] Species frequency estimation
Statistical analysis
Yes
MetaSim Modelling and simulation
Sequence assembly
Mapping
454
Illumina
Sanger
Java Maybe Commercial
Freeware
Metaxa Hidden Markov Model
Sequence analysis
454
ABI SOLiD
Illumina
Ion Torrent
Sanger
Linux
UNIX
Mac OS X
Perl Yes GPLv3
MethMarker Windows
Linux
Mac OS X
Solaris
Java Yes
Methpipe Bisulfite mapping Illumina
Illumina HiSeq
Illumina Solexa
Linux
Mac OS X
C++ Yes GPL (>= 3)
MethylCoder Read mapping
Bisulfite mapping
Illumina Linux
Linux 64
Mac OS X
Python
C
Yes BSD
MetMap Maybe
MeV Sequence clustering
Visualisation
Classification
Differential expression analysis
Yes Artistic License
MG-RAST Annotation Sanger
454
Ion Torrent
PacBio
Illumina
UNIX Perl
C
GO
JavaScript
Python
Yes
MicroRazerS Read mapping Linux C++ No
Microsoft Biology Foundation C# Maybe
MICSA Sequence motif comparison Maybe
Minia Sequence assembly Illumina Linux
Mac OS X
C++ Yes CeCILL
MIP Scaffolder Scaffolding ABI SOLiD
Illumina
Linux C++
Perl
Yes
MIRA Local sequence alignment
Graph reduction
Learning algorithm
Sequence assembly
Read mapping
K-mer counting
Sanger
Illumina
454
PacBio
Ion Torrent
Linux
Mac OS X
UNIX
C++ Yes GPL
MiRanalyzer browser based Java
Perl
Maybe
MiRCat MicroRNA detection Illumina
454
Linux 64
Windows
Mac OS X
Java Yes Custom Licence
MiRDeep Illumina
454
Perl Yes
MiRNAkey Illumina Linux
Mac OS X
Java
Perl
No
MiRProf MicroRNA detection Illumina
454
Linux 64
Windows
Mac OS X
Java Yes Custom Licence
MiRspring Perl
JavaScript
Yes GNU
MirTools Illumina
454
Perl
PHP
Yes
MirTrios Read mapping
Variant calling
De novo mutation detection
Any sequencing platform Linux Perl
PHP
JavaScript
Yes
MISO Any Yes
Mlgt Sequence analysis
Sequence error correction
Sequence contamination filtering
DNA barcoding
Read alignment
454 Windows
UNIX
Mac OS X
R Yes GPL >=2
MMSEQ Mac OS X
Linux 64
C++ Yes
MochiView Genome visualisation
Sequence motif comparison
Linux
Mac OS X
Windows
Java Maybe
MoDIL Illumina Python Yes
MOM Read mapping Illumina No
MOSAIK Sequence assembly Windows
Linux
Mac OS X
C++ Yes Commercial
GPLv2
MotifLab Sequence motif discovery
Sequence contamination filtering
Genome visualisation
Visualisation
Format conversion
Peak calling
platform-independent Java Yes Freeware
MPscan Read mapping Illumina Linux
Mac OS X
C++ Maybe
MrBayes Statistical calculation Cross-Platform Yes
MrCaNaVaR Read depth analysis Illumina POSIX C Yes Commercial
Freeware
MrFAST Read alignment Illumina UNIX C Yes BSD
MrsFAST Read alignment
Mapping
Illumina UNIX C Yes BSD
MTR C++
Matlab
Maybe
MU2A SNP annotation Windows
Linux
Mac OS X
Java No Apache License 2.0
MultiPSQ Peak calling
Peptide mass fingerprint
Classification
Pyrosequencing (QIAGEN) Windows
Linux
C++ Maybe LGPLv3
MUMmer Sequence alignment
Read mapping
Any Linux Yes Artistic License
MUMmerGPU Sequence alignment Any Maybe
MuMRescueLite Mapping Python No MIT
MuSICA 2 Sequence assembly Perl Maybe
Mutascope Variant calling
Analysis pipeline
Illumina
ABI SOLiD
MiSeq
UNIX Perl Yes
MuTect SNP calling Maybe
Myrialign Read mapping
Sequence alignment
Maybe
Myrna Maybe
Mzip File reformatting Maybe
NarrowPeaks Peak calling
Differential Binding
Illumina HiSeq
454
ABI SOLiD
Ion Torrent
Illumina Solexa
Illumina
Linux
Mac OS X
Windows
R Yes Artistic-2.0
NCBI Genome Workbench Visualisation
Genome visualisation
Cross-Platform Yes
Nephele Taxonomic profiling
Functional analysis
Metagenomic Assembly
Roche
Illumina
Yes
Nesoni Sequence alignment Illumina
454
ABI SOLiD
Python Yes
Newbler Sequence assembly
Read mapping
454
Sanger
Ion Torrent
Linux 64 C++ Yes Unknown
Nexalign Read mapping 454
ABI SOLiD
Illumina
UNIX C++
R
No GPL
NextGen Utility Scripts 454
Illumina
ABI SOLiD
Yes
NextGENe Illumina
454
ABI SOLiD
Windows C++ Yes Commercial
Ngs backbone Read mapping
Sequence assembly
Sanger
Illumina
454
UNIX Yes AGPL
NGS-DesignTools Haplotype inference
Modelling and simulation
Maybe
Ngs-pipeline Read mapping
Sequence annotation
Illumina
ABI SOLiD
Linux Perl Yes GPLv3
Ngs.plot Visualisation Any sequencing platform All R
Python
Yes GPL (>= 3)
NGSUtils Sequence contamination filtering
Sequencing quality control
Read pre-processing
Variant calling
Formatting
Illumina
ABI SOLiD
Linux
Mac OS X
Python Yes GPL
NGSView Sequence assembly visualisation Maybe
NOISeq Differential expression analysis Any Maybe
NovelSeq Read mapping
Sequence assembly
Variant calling
Illumina UNIX C Yes BSD
Novocraft Read mapping Illumina
ABI SOLiD
Helicos
Mac OS X
Linux 64
C++ Yes Commercial
Freeware
NPS Python No
NucleR Annotation
Peak calling
Illumina
454
SOLiD
Ion Torrent
Illumina HiSeq
Cross-Platform R Yes LGPLv3
Oases Illumina
ABI SOLiD
454
C Yes GPLv3
Oasis Read mapping
Differential expression analysis
Illumina all supporting JVM JavaScript
Perl
Java
Python
Bash
C
Yes
ODIN Peak calling NGS tested for Linux (Ubuntu) Python Yes
OLego Read mapping
Sequence alignment
Illumina Linux
Linux 64
Mac OS X
C++ Yes GPLv3
Omixon Variant Toolkit Sequence alignment
Sequence assembly
Read mapping
Illumina
Ion Torrent
ABI SOLiD
454
interoperable Yes Commercial
Freeware
Optimus Primer PCR primer design Maybe
PacBio conversion tools File reformatting PacBio Java
R
Python
Yes
PaCGeE Read mapping Maybe Commercial
PALMA Sequence alignment Maybe
PALMapper Read mapping C++ Yes GPLv3
PanGEA 454 Maybe Mozilla Public License
PARalyzer Java Maybe Commercial
Freeware
Partek Genomics Suite Yes
PASH Sequence alignment
Bisulfite mapping
Maybe
PASS Sequence alignment Linux
Windows
C++ Maybe
Patchwork ABI SOLiD
Illumina
Complete Genomics
Linux
Mac OS X
R Yes
PatMaN Read mapping Maybe
PE-Assembler Scaffolding C++ Yes
PeakAnalyzer Java
C++
R
Yes
PeakRanger Peak calling Linux
Mac OS X
C++ Yes Artistic License
PeakSeq C
Perl
Maybe
PeakTrace Base-calling Sanger Windows
Mac OS X
Linux 64
C Yes Commercial
PECAN Sequence alignment No
PEMer Maybe
PERalign Linux C++ Maybe
PerM Read mapping Illumina
ABI SOLiD
Linux C++ Yes Apache License 2.0
Phred Base-calling Sanger Solaris
IRIX
AIX
C Maybe
Phred Phrap Consed Cross match Sequence alignment
Sequence assembly
Base-calling
Local sequence alignment
Sanger Yes
Phymm Maybe
PiCall C Maybe
PICS R Maybe
PileLine Plotting and rendering Java Maybe LGPL
Pindel Split-read mapping
Read mapping
Localised reassembly
Illumina Linux
Mac OS X
Windows
C++ Yes
Pipeline Pilot Read mapping
Sequence analysis
Variant calling
Gene expression analysis
Comparative genomics
Sequence alignment
Sanger
Illumina
454
ABI SOLiD
Linux
Windows
C++
Java
Perl
R
Pilot Script
Yes Commercial
PIQA Sequencing quality control Illumina R Maybe
PoissonSeq Differential expression analysis Any Yes
PolyBayesShort Linux
Linux 64
Maybe
PoolHap Read mapping
Regression analysis
Yes
PoPoolation Perl
R
Maybe
PoPoolation2 Perl
R
Maybe
Post Assembly Genome Improvement Toolkit Sequence assembly validation Linux Yes
PRICE Sequence assembly C++ Yes
PRINSEQ Read pre-processing
Sequence contamination filtering
Sequence trimming
Sanger
Illumina
454
Ion Torrent
PacBio
UNIX
Mac OS X
Windows
Perl Yes GPLv3
ProbeMatch Mapping Illumina Linux
Mac OS X
No
ProbHD Perl
R
Python
No
Promisec Endpoint Manager Security
Endpoint Management
Remediation
Maybe
Proxygenes Read mapping
Annotation
Maybe
Pybedtools Read mapping Windows (Cygwin)
Linux
Linux 64
Mac OS X
Python Yes GPLv2
PyroBayes Base-calling 454 No
PyroMap Read mapping Python Maybe
PyroNoise 454 Maybe
QCALL Maybe
Qpalma Sequence alignment Illumina
454
Python
C++
Maybe
QRidge Sequence assembly Any sequencing platform Maybe
QSeq Sequence alignment
Visualisation
Peak calling
Roche NimbleGen
Illumina
454
ABI SOLiD
Helicos
Sanger
Windows 7 64-bit or Higher
Mac OS X 10.7
10.8
or 10.9 with Parallels Desktop
Yes Commercial
QSRA Sequence assembly No
QuadGT SNP calling
Variant calling
Any Java Yes
Quake Sequence error correction Illumina Maybe
QualiMap Sequencing quality control Maybe
QUAST Visualisation
Sequence assembly validation
Any Linux
Mac OS X
Python
C
Perl
Yes GPLv2
QuEST C++ No GPLv2
Quip File reformatting any C Yes BSD (3-clause)
R2R Sequence alignment Perl Maybe
R453Plus1Toolbox 454 R Yes
RACA Maybe
RApiD Perl
C++
Maybe GPLv3
RAPSearch Sequence alignment C++ Yes GPLv3
RAST Annotation
Genomics
Yes
Ray Sequence assembly Illumina
454
Linux
POSIX
C++ Yes GPL
RazerS Local sequence alignment
Read mapping
Sanger
Illumina
454
UNIX
Mac OS X
Windows
C++ Yes GPLv3
RDiff Sequence alignment
Differential expression analysis
Illumina HiSeq
Illumina Solexa
Illumina
Linux
Mac OS X
Python
Matlab
Yes Open Source
RDP Pyrosequencing Pipeline Sequence alignment
Formatting
454 browser based Maybe
Readaligner Read mapping Maybe
ReadDepth R Maybe Apache License 2.0
REAL Mapping Linux C++ Maybe GPLv3
Reaper Sequence contamination filtering
Adapter removal
Sequence trimming
DNA barcoding
Sequencing quality control
Illumina
454
Linux
UNIX
Mac OS X
C Yes GPLv3
Reconciliator Sequence assembly Linux Perl Maybe
RECOUNT Expectation Maximisation Illumina Linux C++ Yes GPL
RefCov No
Repitools Sequencing quality control
Visualisation
Methylation calling
Statistical calculation
R Yes LGPL
Reptile Sequencing quality control Illumina C++ Yes GPL Boost
ReSeqSim Read mapping
Simulation
Maybe
RGA Sequence assembly Illumina Maybe
RiboPicker Read pre-processing
RRNA filtering
Sanger
Illumina
454
Ion Torrent
PacBio
UNIX
Mac OS X
Perl
C
Yes GPLv3
RMAP Read mapping
Bisulfite mapping
Linux
Mac OS X
Maybe GPLv3
RNA Read mapping Illumina
ABI SOLiD
454
Linux
UNIX
Windows
Mac OS X
C++ Yes GPLv3
RNA-MATE Maybe
RNASEQR Read mapping Maybe
Rnnotator Maybe Commercial
Freeware
RobiNA Differential expression analysis Illumina Windows
Linux
Mac OS X
Java
R
Yes GPL
Rolexa Base-calling R Maybe
RSAT peak-motifs Sequence motif discovery
Sequence motif recognition
Sequence motif comparison
Any UNIX
Mac OS X
Linux
Perl
CGI
Python
C
Yes Commercial
Freeware
RSEM C++ Maybe
RSEQtools Mac OS X
UNIX
Linux
C Yes Creative Commons - Attribution; Non-commercial 2.5
Rsolid Base-calling ABI SOLiD R
C
Maybe
Rsubread Read mapping
Read summarisation
Quality assessement
ABI SOLiD
Illumina HiSeq
Illumina Solexa
Ion Torrent
454
Linux 64
Mac OS X; x86 64
Mac OS X
R
C
Yes GPLv3
RUbioSeq Variant calling Illumina
ABI SOLiD
UNIX Perl Yes
S-MART Linux
Mac OS X
Windows
Python
Java
Yes
SAMMate Sequence analysis Windows
Mac OS X
Java Yes GPLv3
Samscope Visualisation
Read mapping
Any POSIX
Linux
C++ Yes AGPL
SAMStat Sequencing quality control Illumina
Helicos
454
UNIX C Maybe GPLv3
SAMtools Modelling and simulation
Sequence assembly visualisation
C Yes MIT
Savant Genome Browser Visualisation
Sequence alignment visualisation
Illumina
454
Sanger
Windows
Linux
all supporting JVM
Mac OS X
Java Yes Apache License 2.0
Scaffolder Scaffolding Linux
Mac OS X
Ruby Yes MIT
ScaffViz Sequence assembly 454
Illumina
Anything that can be assembled with Celera or Newbler
Maybe
SCALCE File reformatting Illumina Linux 64
Linux
C Yes
SCARF Sequence assembly Maybe GPLv3
Scripture Illumina Maybe
SEAL Read mapping Illumina Python
C++
Java
Yes GPLv3
SEECER Sequence error correction Illumina
454
Ion Torrent
PacBio
C Yes
SEED Sequence clustering Illumina Mac OS X
Linux
Windows
C++ Yes
Segemehl Mapping C
C++
Maybe
Segtor Annotation
SNP annotation
Linux
Mac OS X
Perl
C
Maybe Non-commercial
Seq2HLA Read mapping
Genetic variation analysis
Illumina Unix
Mac OS X
Python
R
Yes
SeqAn Sanger
Illumina
454
UNIX
Mac OS X
Windows
C++ Yes BSD (3-clause)
SeqBuster Read mapping
Annotation
Illumina
454
Mac OS X
Linux
Java
R
Yes Commercial
Freeware
SeqCons Sequence assembly Linux
Windows
No
SeqEM Expectation Maximisation Maybe
SeqGSEA Statistical calculation
Functional analysis
Functional enrichment
Any any R Yes GPL (>= 3)
SeqMan NGen Read mapping
Sequence assembly
Sequence alignment
Ion Torrent
Roche 454
Pacific Biosciences
Illumina
Sanger
Windows 7 64-bit or Higher
Mac OS X 10.7
10.8
or 10.9
Linux Ubuntu 12.04
Linux CentOS 6.5
Yes Commercial
SeqMap Read mapping Mac OS X
Windows
Linux
Maybe
SeqMINER Any platform-independent Java Yes GPLv3
SeqMonk Visualisation
Sequence assembly visualisation
Statistical calculation
Sequence alignment visualisation
Windows
Mac OS X
Linux
Java Yes GPLv3
SeqPrep Illumina POSIX C Yes MIT
SeqSaw Read mapping
Sequence alignment
Illumina Linux C++ Yes GPL
SeqSeg Matlab Maybe
SeqSite Peak calling Illumina HiSeq
454
ABI SOLiD
Ion Torrent
Illumina Solexa
Illumina
Linux
Mac OS X
Windows
C
C++
Yes GPL
SeqSolve Differential expression analysis
Ab-initio gene prediction
Quality control
Illumina
ABI SOLiD
454
Ion Torrent
Helicos
PacBio
Any
Illumina HiSeq
Illumina Solexa
Windows
Linux
Yes Commercial
SeqSphere+ Sequence assembly
Read mapping
Variant calling
Sanger
Illumina
454
Ion Torrent
PacBio
Windows
Linux 64
Java Yes Commercial
SeqTrim Sequence trimming Maybe
Sequedex Sequence analysis
Sequence annotation
Illumina HiSeq
Illumina Solexa
Illumina
Linux 64
Mac OS X
Java
Python
Yes Commercial
Freeware
SequenceVariantAnalyzer Annotation
Genome visualisation
SNP calling
Linux 64 Java Yes
Sequencher Sequence assembly
Sequence alignment
454
Illumina
ABI SOLiD
Ion Torrent
Sanger
Windows
Mac OS X
Yes Commercial
SeqWare Laboratory information management
Workflows
Linux Java Yes GPLv3
SeqWords K-mer counting Perl Maybe Perl artistic licence
SESAME Windows
Linux
Maybe GPLv3
SEWAL Illumina Maybe
Sff2fastq Conversion 454 Linux Yes
SGA Sequence assembly Illumina Linux C++ Yes GPLv3
SHARCGS Sequence assembly Linux Perl Maybe
SHE-RA Sequence error correction Illumina Maybe Open Source
Sherman Modelling and simulation Illumina
ABI SOLiD
Linux
Mac OS X
Perl Yes GPLv3
ShoRAH Haplotype inference
Read mapping
454
Illumina
Linux
Mac OS X
Yes GPLv3
Shore Mapping Illumina
ABI SOLiD
Linux
Mac OS X
POSIX
Yes
SHOREmap Illumina
ABI SOLiD
Perl
R
Yes GPLv3
ShortFuse C++
Python
Maybe
ShortRead R Yes
SHORTY Sequence assembly ABI SOLiD C++
Perl
No
SHRAP Sequence assembly Maybe
SHREC Sequencing quality control
Sequence error correction
Illumina Java Yes
SHRiMP Read mapping ABI SOLiD
Helicos
454
Illumina
Maybe
Sibelia Variant calling C++ Yes GPL
SICER Sequence contamination filtering Python Yes
SiLoCo Gene expression profiling Illumina
454
Linux 64
Windows
Mac OS X
Java Yes Custom Licence
Sim4cc Read mapping UNIX
Linux
C++ Yes GPLv2
SimNext Modelling and simulation Illumina Perl No
SimSeq Modelling and simulation Illumina POSIX Java
C
Yes MIT
Sissrs Peak calling Linux
UNIX
Perl Maybe
Skewer Read pre-processing
Adapter removal
Sequence trimming
Read mapping
Illumina
Illumina HiSeq
Illumina Solexa
Linux 64 C++ Yes
Slider Mapping Illumina Java Maybe
SlideSort Clustering Linux
Windows
C++ Yes
SLOPE C++ Maybe
SmashCommunity 454
Sanger
Maybe
SNIP-Seq Python Maybe
Sniper UNIX
Mac OS X
C
Python
Maybe
SNP-o-matic Read mapping Illumina C++
C
Maybe
SNPsea Enrichment *NIX C++
R
Python
Yes GPLv3
SNPSeeker Illumina C No
SNVer Windows
Linux
Mac OS X
Java Maybe
SNVMix C Maybe MIT
SOAP Sequence alignment
Read mapping
Genome indexing (Burrows-Wheeler)
UNIX C++ Maybe
SOAPdenovo Sequence assembly Illumina Linux
Mac OS X
Yes GPLv3
SOAPfusion Illumina HiSeq
Illumina Solexa
Illumina
Linux 64 Perl
C++
Yes
SOAPsnp C
C++
Yes
SOCS Read mapping
Bisulfite mapping
ABI SOLiD POSIX C++ Maybe GPLv3
Solas R Maybe
Sole-Search Illumina Java No
SolexaQA Sequencing quality control
Sequence trimming
Illumina
454
Mac OS X
UNIX
Perl
R
Yes GPLv3
SolexaTools Laboratory information management Illumina Java No
SOLID software tools ABI SOLiD Yes Commercial
SomaticCall Maybe
SOPRA Sequence assembly
Scaffolding
ABI SOLiD
Illumina
Yes GPL
Spiral Genetics Sequence alignment
File reformatting
Read mapping
Illumina Linux
Mac OS X
Windows
C++ Yes Commercial
SpliceGrapher Visualisation Any Maybe
SpliceMap Read mapping Linux Python
C++
Yes
SplicePlot Visualisation Maybe
SpliceTrap Statistical calculation Illumina UNIX
Linux
C++
Perl
Yes
SplicingViewer Mapping Illumina Linux
Windows
Mac OS X
Java Yes GPL
Commercial
BioLicense
LGPL
BSD License
SPLINTER C
C++
Yes Commercial
Freeware
SplitSeek ABI SOLiD Perl Maybe GPL
SPP Peak calling Illumina
454
Sanger
SOLiD
Ion Torrent
R Maybe
SR-ASM Sequence assembly 454 Linux
UNIX
C++ Maybe
SRAdb R Maybe
SRMA Localised reassembly Illumina
ABI SOLiD
454
Java
C
Yes GPL
SSA Sequence analysis
Sequence motif comparison
Sequence motif discovery
Linux
Mac OS X
Fortran F77
C
Perl
Yes GPL
SSAHA Sequence alignment
Local sequence alignment
Sanger
454
Illumina
Linux
Mac OS X
Yes Commercial
Freeware
SsahaSNP Mac OS X
Linux 64
Linux
Solaris
Compaq Alpha
Maybe
SSAKE Sequence assembly Linux Perl Maybe GPLv2
SSPACE Scaffolding Illumina
ABI SOLiD
454
Windows
Linux
Mac OS X
Perl Yes
STADEN Sequence assembly
Sequence alignment
Visualisation
Sanger
454
Illumina
Linux
Windows
Mac OS X
UNIX
C
C++
Tcl
Fortran
Yes BSD
Stampy Read mapping Illumina Linux Python Yes Commercial
Freeware
Standalone hamming Sample Barcoding Python Maybe
Standardized Velvet Assembly Report Visualisation Any R
Perl
No GPLv3
STAR Sequence alignment Illumina
454
Sanger
Ion Torrent
PacBio
Linux
Unix
Mac OS X; x86_64
C++ Yes GPLv3
Strelka Variant calling Linux Perl Yes
Subjunc Read alignment Illumina HiSeq
ABI SOLiD
Ion Torrent
454
Yes
Subread Read mapping Illumina
ABI SOLiD
Ion Torrent
454
Linux 64
Mac OS X
Mac OS X; x86 64
C Yes GPLv3
SuccinctAssembly Linux Yes
SUDS genome browser Genome visualisation C++ Maybe GPLv2
Suffixerator Genome indexing (suffix arrays) Linux Maybe
Supersplat Sequence assembly Maybe C++
SUTTA Maybe Commercial
Freeware
SVDetect Perl Maybe
SVMerge Illumina Perl Yes
Swalign Sequence alignment C Maybe MIT
SWAP454 454 Maybe
SwDMR Methylation calling Any Linux
UNIX
Perl
R
Yes GPLv3
Swift Base-calling Linux C++ Maybe LGPL
SWT Maybe
SXOligoSearch Sequence alignment Illumina No
Syapse Differential expression analysis
Exome analysis
Sequence analysis
Variant classification
Visualisation
Ontology comparison
Any
Illumina
Ion Torrent
Affymetrix
Complete Genomics
Sanger
Yes
Syzygy Python
R
Yes
T-lex Perl Maybe
Ta-si prediction Phase pattern prediction Illumina
454
Linux 64
Windows
Mac OS X
Java Yes Custom Licence
Tablet Sequence assembly visualisation Illumina
454
Sanger
Windows
OS X
Linux
Java Yes BSD
TagCleaner Sequence trimming Sanger
Illumina
454
Ion Torrent
PacBio
UNIX
Mac OS X
Windows
Yes GPLv3
TagDust Sequencing quality control Illumina Solaris
UNIX
Linux
C Yes GPL
Taipan Sequence assembly Maybe
Tally Sequence redundancy removal
Read pre-processing
Sequence contamination filtering
Illumina Linux
UNIX
Mac OS X
C Yes GPLv3
Tallymer K-mer counting
Genome indexing (suffix arrays)
Linux Maybe
TAPyR Read mapping 454
Illumina
Ion Torrent
C Yes GPL
TASE Illumina Java Maybe
TASR Sequence assembly Perl Yes GPLv2
TEQC Sequencing quality control R Maybe
TileQC Sequencing quality control R Maybe
TiMat2 Genotyping Java No BSD
TMAP Read mapping Ion Torrent Yes
TMAP Read mapping Ion Torrent Yes
TopHat Sequence alignment
Mapping
Illumina
SOLiD
454
Linux
Unix
C++ Yes Boost
TopHat-Fusion Yes
TOTALRECALLER Base-calling Illumina Linux Maybe Commercial
Freeware
Tracembler Sequence assembly Linux Maybe
Trans-ABySS Maybe BCCA (academic use)
Trimmomatic Sequence trimming
File reformatting
Sequencing quality control
Illumina Maybe
Trinity Transcriptome assembly Illumina Linux Java
C++
Maybe
Tripal Visualisation PHP Yes Open Source
Tview Visualisation C Yes BSD
MIT
UGENE Sequence parsing ABI SOLiD
Sanger
Illumina
454
Linux
Windows
Mac OS X
C++ Yes GPLv3
UnoSeq Java Maybe
USeq Java Yes BSD
V-Xtractor Statistical calculation Any UNIX Perl Yes GPL
VAAL Sequence alignment Maybe
VAAST Variant prioritisation Any Yes Commercial
Freeware
Variant Effect Predictor SNP annotation Perl Yes
VariantClassifier SNP annotation Maybe
Variation toolkit SNP annotation Linux C++ Yes GPLv3
VariationHunter Read mapping
Variant calling
Illumina UNIX C Yes
VARiD Statistical calculation ABI SOLiD
Illumina
454
Sanger
C Yes GPLv3
VarScan Java Yes
VCAKE Sequence assembly
K-mer counting
Linux
Mac OS X
Perl
C
No GPL
Vcflib C++ Yes MIT
VCFtools C++ Maybe GPLv3
Vectorfriends Sequence alignment
Sequence assembly
Annotation
Sequence alignment visualisation
Visualisation
Sanger Windows Java Yes Free for academic use; Commercial
Velvet Sequence assembly
Sequence assembly (de-novo assembly)
Illumina
454
ABI SOLiD
Yes GPL
VelvetOptimiser Perl Yes GPLv2
Vicuna Illumina
454
Ion Torrent
POSIX C++ Yes
VIP Mapping
SNP annotation
SNP detection
454 Linux Perl
MySQL
Maybe LGPL
ViralFusionSeq Read mapping
Read pre-processing
Sequence alignment
Sequence assembly
Illumina Linux Perl Yes GPLv3
VirusHunter Maybe
VirusSeq Read mapping Illumina Perl Maybe Unknown
VisSR Visualisation Illumina
454
Linux 64
Windows
Mac OS X
Java Yes Custom Licence
Vmatch Read mapping Linux Yes Commercial
WebApollo Annotation Requires Tomcat server JavaScript
Perl
Java
Yes Open Source
WebPrInSeS ABI SOLiD
Illumina
454
browser based Maybe
WHAM Read mapping Illumina Yes GPLv3
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