- Speed up sequence alignments using your video card!
- Bioinformatics
- Software packages for next gen sequence analysis
- SOAP: short oligonucleotide alignment program.
- Sample short read data set?
- Bioconductor for next-gen sequencing anlaysis?
- Preliminary benchmark of different alignment programs
- solexa small rna questions
- Who is Geospiza?
- New version of Solexa GA pipeline tool
- FindPeaks 3.1.3 (alpha) - ChIP-Seq and UCSC-compatible short-read wig track creator
- pooling genes in a solexa lane
- ISMB 2008 SIG on Algorithms for Next Gen Sequencing
- Quality score threshold?
- Converting FASTQ to RMAP prb files
- SoftGenetics NextGENe
- CLC Genomics Workbench
- short reads missed by aligners
- Solexa data to fasta
- eland realign file
- Illumina's PRB file to FastQ
- indels using single end short reads!
- where can I download eland program?
- Fasta to Ace conversion
- Using pbShort
- Maq and export format
- SeqMan NGen
- New Short Read Aligner
- Desktop computer specs for routine analyses? Post your rig
- Questions about solexa quality score
- Questions about solexa quality score!
- compare solexa and 454
- Plug for new ChIP-Seq Package and the Integrated Genome Browser
- Heavy read stacking on the solexa platform
- question about ssaha
- Paired-end Illumina data
- FindPeaks (ChIP-Seq) update
- Convert euler-sr output to amos-bank
- population genetics parameter estimation of solexa population sequencing
- Human reference sequence and tools like MAQ
- Interpretation of Euler-SR assembly (454 transcriptome)
- SNP Allele-Frequency Determination in Pooled DNA Samples using solexa
- de novo assembly of transcriptomes
- Any programme can estimate SNP frequency ?
- What does Illumina raw data look like?
- Allpaths installation and usage
- Bioinformatics at COMSATS IIT
- Reference Genome
- spike-in data set
- Genomatix offerings
- reference set for analyzing illumina DpnII tags?
- How to detect real deletion or gaps in sequencing projects
- retrieve gene name
- de novo hybrid assembly
- An HMM approach to genome-wide identification of differential histone modification si
- different Illumina convention in fastq files?
- Mapping benchmarks of the GMS
- maq on a mac
- how to use soap?
- Public Helicos Data
- SOAP on Mac Pro
- Gene Expression Tag Table Software Now Available
- Running MAQ SNP/Indel detection/Assembly Tools on short aligners
- what is a paired-end read?
- Velvet de novo assembly to amosvalidate
- ZOOM released (supporting both Illumina data and ABI SOLiD data)
- Alta-Cyclic
- what is wrong with my MAQ?
- ShortRead package
- ChIP-Seq reads correlated/distance to with TSS/promoter etc.
- Methods for comparing RNA sequencing libraries?
- MAQ and indel detection
- Transcriptom assembly
- MAQ SNP calling
- MAQ mapping quality scores
- FindPeaks is now OpenSource!
- installation can't find TRF programme
- export from MAQ to EagleViewer
- finding polymorphisms by large sequence alignments
- LastGen Assembly
- Data retention
- Swift: Open source primary data analysis for Next-gen sequencers
- new basecallers since Bustard
- RNA-seq and normalization numbers
- from CGH arrays to genome map
- Analysis of Solexa multiplexed data
- SNP/Mutation Detection Using Illumina Paired-end Data
- why reads piled up at repeat region?
- eland_tag - 3' tag analysis
- Maq SNP filtering script bug?
- Eland-to-Bed algorithm
- Hybrid sequencing assembly visualization
- eland2maq
- alignment reference
- SNP calling on 454 data
- ChipSEQ on Solexa (low % align, unusable reads)
- Quality score graph
- Bowtie, an ultrafast, memory-efficient, open source short read aligner
- SOLiD alignment browser
- Maq problems getting started
- MAQ .map alignment format converter
- How to use MAQVIEW?
- How to make great wiggle plots and Seq figures
- Structural Variations
- Maq SNP calls from a large pool
- Slider - Maximum use of probability information for alignment of short sequence reads
- paired-end reads and shotgun
- Inversions
- BFAST: Blat-like Fast Accurate Search Tool for Large-Scale Genome Resequencing
- ABI Color Space to Bases
- CisGenome -- an integrated tool for ChIP-seq data analysis
- eagleview discrepancy search
- Analysis for Paired end reads
- SNP Frequency
- start position of reads and its distribution
- Pipeline Illumina question
- Segmentation Fault from Maq's .map files
- maq map - Assertion 'matches' failed
- 1000 genomes fastq format
- ChIP seq
- Need comment on CLCbio software
- LIMS Systems
- Paired end solexa (goat/gerald) pipeline
- Reference seq. on MAQviewer
- Help installing Illumina pipeline 1.0
- Input files for the Celera Assembler?
- indelpe from MAQ
- How to estimate the transcription level?
- still got Maq problems
- Celera Assembler (WGS) - splice site file?
- de novo 454 assembly
- Assess the quality of solexa reads
- new EULER-SR
- Maq output: assemble.log file contains what?
- MAQ Scores & Quantify maq alignments?
- Solid VS Solexa
- a question about fasta quality.
- GapPipeline v1.0 on Mac OS X 10.5.5
- SAM: a generic alignment format
- Raw solexa data processing
- Convert MAQ or Bowtie output to Vmatch
- MAQ: finding the stop position of an alignment
- Solexa anomaly.txt for structual variants
- ALLPATHS compiling issues
- Novoalign V2.0 Released
- how to view a 600MB wig file
- Gene Calling
- Illumina de novo assembly with quality values
- MAQ Alignment Depth
- New software: G-Morse : Annotating genomes with massive-scale RNA-sequencing
- Assembling .sff files from 454 and finishing
- Eland to ACE
- Tag (string) Compression Techniques
- Alignment Questions
- MapView: a viewer for short reads alignment
- Cisgenome
- Help - MAQ getting started
- ChIP-Seq Challenge
- A question about alignment depth
- Alignment of Long SAGE tags
- miRNA aligning/counting
- Bowtie print read length
- Fraction of reads incorporated in Velvet assemblies
- BS-Seq Public /Sharing Data
- Shore
- CAP3 output *.ace in EagleView?
- Assembling pooled BACs from 454 data
- About Data Format and Eland Input
- Amplification region in genome
- Solexa pipeline
- How to convert .txt file to .bed or .gff, How can we use chip seq data in R software
- Tool for Sorting PRB file
- Updated How to convert .txt file to .bed .GFF or .BAR file format,
- problems concerning seq.txt and prb.txt
- Vaal
- User friendly ChIP-Seq software
- Reference genome for MAQ - split reference genome by chromosome or not?
- bowtie - windows instalation
- Maqview Reference Sequence
- What is the difference between sol2std and sol2sanger
- illumina GA2, 75bp paired-end data
- MAQ - segmentation error
- help - buffer overflow problem of Maq in Ubuntu 8.10
- What NextGen LIMS do you use?
- Parallel Processing for Sequence Analysis
- SOAP output format - description?
- Question about pthred quality
- CpG Islands Vs CHIP-Seq data
- SOAP vs Bowtie output
- MAQ mapstat error rate
- How to using euler-sr to assebling 454 seq?
- maq with no mismatches
- Eland for Tag Greater than 32 basepair
- How to trim the adaptor sequence from the solexa small RNA sequencing data?
- Data Format Question
- .bam alignment format from 1000 Genomes Project
- Viewing paired-end inconsistencies in 454 scaffolds
- Strange maq 7.1 problem
- Eland output from SeqMap
- chord->getLength Newbler error
- All chromosomes and maq
- Eland for different sizes
- view .wig files
- MAQ error
- Maq problem: 0 raw reads mapped
- PubMed: PASS: a Program to Align Short Sequences.
- Setting up a 454 Bioinformatics center
- maq compile error on Ubuntu
- Fastq quliaty score and MAQ output quality score
- mapping 454 reads to a reference genome
- Solexa.abi and 454 seq data.
- long repeated elements in a bacterial genome
- Maq Alignment Coordinates
- de novo assembly on 3.5Gbp data -- computational speed!!??
- comparing results from two different reference genomes
- Alignment of ABI solid reads and 454 reads
- BOWTIE output problems
- Two Version of Solexa Quality Score Formula
- maq pair end alignment error
- sff_extract paired end extraction error
- MAQ and small RNAs
- Burrows-Wheeler Aligners for Colorspace?
- INDEL searches!
- Uniquely mapped short reads (MAQ)
- Transcriptome assembly using solexa reads
- Manually correct heterozygous indels
- So many software for alignment!!!
- Euler SR
- Pseudocode for Generating Synthetic Tags with Error Rate
- Convert MAQ,SOAP alignment result to ACE format
- why is paired-end alignment support so important
- maq mapcheck
- A list of available sequence annotation tools?
- Binning of aligned mRNA-reads into gene models
- WIG files
- (a) Background Read Distribution (b) Spike-ins
- ISAS Alignment Software
- Maq multiple map output (-H)
- Adequate coverage for genome wide pair end sequencing
- Which quality score?
- velvet
- Perfect match disagreement between bowtie and BLAT on human genome
- BFAST - Alignment for ABI or Illumina sequencing - with qualities
- GBrowse and Chip-seq Peaks
- Software for Sorting SNPs/ InDels by Affect?
- FindPeaks output
- Segmentation fault with Mosaik
- Storage Gotchas
- Coverage display?
- Problem with adding 454 reads with cross_match