Tools   Select Another Resource Report Type

http://maq.sourceforge.net/

A set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way.

Proper citation: Maq (RRID:SCR_005485) Copy   

•   Source: SciCrunch Registry

http://chipexo.sourceforge.net/

A bioinformatics tool dedicated to analyze ChIP-exo data: 1) Sequencing depth normalization and nucleotide composition bias correction. 2) Signal consolidation and noise reduction. 3) Single base resolution border detection. 4) Border matching.

Proper citation: MACE (RRID:SCR_005520) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/p/treq/home/Home/

A software read mapper for high-throughput DNA sequencing reads, in particular one to several hundred nucleotides in length, and for large edit distance between sequencing read and match in the reference genome. It can cope particularly well with indels for single-best hit recall of 200nt reads simulated from the human reference genome. TreQ performs best at a running time comparable to BWA at large edit distance settings.

Proper citation: TreQ (RRID:SCR_005505) Copy   

•   Source: SciCrunch Registry

http://geckoe.sourceforge.net/

A complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community.

Proper citation: Gecko (RRID:SCR_009001) Copy   

•   Source: SciCrunch Registry

http://scalce.sourceforge.net/Home

A FASTQ compression tool that uses locally consistent parsing to obtain better compression rate.

Proper citation: SCALCE (RRID:SCR_009658) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bycom/

A software which can perform methylcytosine calling from BS-seq (WGBS and RRBS), and permits either unmapped reads (FASTQ) or mapped reads (SAM/BAM) to be used as the input data. Certain SNPs (C>A/G) can also be selected in the output.

Proper citation: Bycom (RRID:SCR_000659) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/cnv/

Software for a web-enabled platform for analyzing genome variation such as copy number variation (CNV).

Proper citation: CNV Workshop (RRID:SCR_012635) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/p/krona/home/krona/

Software that allows hierarchical data to be explored with zoomable pie charts.

Proper citation: Krona (RRID:SCR_012785) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/acaciaerrorcorr/?source=navbar

Accurate error-correction of amplicon pyrosequences.

Proper citation: Acacia (RRID:SCR_012896) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ibdld/

A C++ software program for multipoint IBD estimation based on high density SNP genotype data.

Proper citation: IBDLD (RRID:SCR_013043) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/solsnp/

A Java-based DNA variant calling tool for Next-Generation Sequencing alignment data.

Proper citation: SolSNP (RRID:SCR_013045) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/tumorhats/

A software tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next generation sequencing tumor data.

Proper citation: HATS (RRID:SCR_013044) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/chipotle-perl/

A peak-finding algorithm used to analyze ChIP-chip microarray data.

Proper citation: ChIPOTle Peak Finder (RRID:SCR_012991) Copy   

•   Source: SciCrunch Registry

http://trinityrnaseq.sourceforge.net/

Software for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.

Proper citation: Trinity (RRID:SCR_013048) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ngspeanalysis/

A pipeline using open-source tools which can implement a set of pair ended Next-generation sequencing analysis, include short reads alignment, high-quality variation genotype calling and variants annotation.

Proper citation: NGSpeAnalysis (RRID:SCR_013040) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/lofreq/

A fast and sensitive variant-caller for inferring single-nucleotide variants (SNVs) from high-throughput sequencing data.

Proper citation: LoFreq (RRID:SCR_013054) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/genecounter/

A computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression of eukaryotes, prokaryotes, as well as organisms with no available genome reference sequence.

Proper citation: GENE-counter (RRID:SCR_013056) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/rnacompass/

A web-based GUI distributed computational pipeline, provides all-in-one functionality including human transcriptome quantification and the typical endogenous RNA-Sequencing analysis along with the investigation of exogenous sequences.

Proper citation: RNA CoMPASS (RRID:SCR_013058) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/snptools/

A suite of software tools that enables integrative SNP analysis in next generation sequencing data with large cohorts.

Proper citation: SNPTools (RRID:SCR_013052) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/swiftng/

An open source package for primary data analysis on next-gen sequence data from images to basecalls. Currently Swift is targeted toward Solexa/Illumina sequencing, but is designed to be platform agnostic.

Proper citation: Swift (RRID:SCR_013018) Copy   

•   Source: SciCrunch Registry