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http://sourceforge.net/projects/acaciaerrorcorr/?source=navbar
Accurate error-correction of amplicon pyrosequences.
Proper citation: Acacia (RRID:SCR_012896) Copy
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
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
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
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
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
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
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
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
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
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
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
http://sourceforge.net/projects/cloudaligner/
A map/reduce based application for mapping short reads generated by the next-generation sequencing machines.
Proper citation: CloudAligner (RRID:SCR_012962) Copy
http://sourceforge.net/projects/tracetuner/
Software tool for base and quality calling of trace files from DNA sequencing instruments.
Proper citation: TraceTuner (RRID:SCR_013019) Copy
http://sourceforge.net/projects/seqminer/
Software for a genome wide mapping data interpretation platform for NGS (ChIPSeq).
Proper citation: seqMINER (RRID:SCR_013020) Copy
http://sourceforge.net/projects/mireap/
A software tool which can be used to identify both known and novel microRNAs from small RNA libraries deeply sequenced by Solexa/454/Solid technology.
Proper citation: MIREAP (RRID:SCR_013025) Copy
http://sourceforge.net/projects/msa-edna/
Software for Multiple Sequence Alignment for Transcription Factor Binding Sites using Di nucleotides dependencies and relying on Free Interaction energies between neighbouring DNA bases to stabilise substitution energy of the alignment.
Proper citation: EDNA (RRID:SCR_012981) Copy
http://sourceforge.net/projects/samzip/
An encoding and decoding tool for Sequence Alignment/Map (SAM) files.
Proper citation: SAMZIP (RRID:SCR_012980) Copy
http://sammate.sourceforge.net/
An open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate.
Proper citation: SAMMate (RRID:SCR_013037) Copy
http://sourceforge.net/projects/flexbar/
Flexible barcode and adapter removal for sequencing platforms.
Proper citation: Flexbar (RRID:SCR_013001) Copy
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