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http://sourceforge.net/projects/pennseq/
Software for isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution. Instead of making parametric assumptions, they give adequate weight to the underlying data by the use of a non-parametric approach. The rationale is that regardless what factors lead to non-uniformity, whether it is due to hexamer priming bias, local sequence bias, positional bias, RNA degradation, mapping bias or other unknown reasons, the probability that a fragment is sampled from a particular region will be reflected in the aligned data. This empirical approach thus maximally reflects the true underlying non-uniform read distribution.
Proper citation: PennSeq (RRID:SCR_001763) Copy
Software environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS.
Proper citation: R Project for Statistical Computing (RRID:SCR_001905) Copy
https://github.com/benedictpaten/pecan
A Java consistency based multiple sequence alignment software program.
Proper citation: Pecan (RRID:SCR_001909) Copy
http://www.agcol.arizona.edu/software/tcw/
Software package for assembling, annotating, querying, and comparing transcript and expression level data that consists of two parts: * singleTCW (sTCW): Single transcript sets or assemblies; annotation; differential expression (EdgeR, DEGSeq, DESeq, GoSeq) * multiTCW (mTCW): Comparison of multiple transcript sets; ortholog grouping (e.g., OrthoMCL) It has been tested on Linux and uses Java, mySQL and optionally R.
Proper citation: TCW (RRID:SCR_001875) Copy
https://github.com/JialiUMassWengLab/TEMP
Software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data.
Proper citation: TEMP (RRID:SCR_001788) Copy
https://github.com/nicolazzie/AffyPipe
An open-source software pipeline for Affymetrix Axiom genotyping workflow.
Proper citation: AffyPipe (RRID:SCR_002032) Copy
https://github.com/adrlar/CanSNPer
Software that is a hierarchical genotype classifier of clonal pathogens.
Proper citation: CanSNPer (RRID:SCR_001980) Copy
http://sourceforge.net/projects/denovoassembler/files/
Software that assembles reads obtained with new sequencing technologies (Illumina, 454, SOLiD) using MPI 2.2.
Proper citation: Ray (RRID:SCR_001916) Copy
http://cakesomatic.sourceforge.net/
A bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone.
Proper citation: Cake (RRID:SCR_002133) Copy
An alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data.
Proper citation: RUM (RRID:SCR_008818) Copy
https://github.com/armintoepfer/QuasiRecomb/releases
A jumping hidden Markov model that describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data.
Proper citation: QuasiRecomb (RRID:SCR_008812) Copy
Merging Two Gene Expression Studies via Cross Platform Normalization.
Proper citation: XPN (RRID:SCR_008845) Copy
http://tvap.genome.wustl.edu/tools/music/
A set of tools aimed at determining the significance of somatic mutations discovered within a given cohort of cancer samples, incorporating the cohort''s alignment data, variant lists and any relevant clinical data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MuSiC (RRID:SCR_008792) Copy
http://bioinfo.au.tsinghua.edu.cn/software/seqsaw/
A package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data.
Proper citation: SeqSaw (RRID:SCR_009185) Copy
http://mendel.stanford.edu/sidowlab/downloads/quest/
A Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitation (ChIP-seq) experiments.
Proper citation: Quantitative Enrichment of Sequence Tags (RRID:SCR_004065) Copy
http://www.brl.bcm.tmc.edu/pash/pashDownload.rhtml
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.
Proper citation: Pash 3.0 (RRID:SCR_004078) Copy
http://epigraph.mpi-inf.mpg.de/WebGRAPH/
A software for genome and epigenome analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: EpiGRAPH (RRID:SCR_004326) Copy
http://sourceforge.net/projects/insertionmapper/
A pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. It consists of four independently working modules: Data Preprocessing, Database Modeling, Dimension Deconvolution and Element Mapping. This pipeline tool is applicable to scenarios requiring analysis of the tremendous output of short reads produced in NGS sequencing experiments of targeted genome sequences.
Proper citation: InsertionMapper (RRID:SCR_004163) Copy
https://bcbio-nextgen.readthedocs.org/en/latest/
A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis.
Proper citation: bcbio-nextgen (RRID:SCR_004316) Copy
http://genome.gsc.riken.jp/osc/english/dataresource/
A program to eliminate artifactual reads from next-generation sequencing data sets.
Proper citation: TagDust (RRID:SCR_004175) Copy
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