Tools   Select Another Resource Report Type

http://contra-cnv.sourceforge.net/

A tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data.

Proper citation: CONTRA (RRID:SCR_010814) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/breseq/

A computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data intended for haploid microbial genomes.

Proper citation: breseq (RRID:SCR_010810) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/cancer/cga/mutsig

Software that analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes.

Proper citation: MutSig (RRID:SCR_010779) Copy   

•   Source: SciCrunch Registry

http://svdetect.sourceforge.net/Site/Home.html

Software application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies. This tool aims to identify structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale. It is compatible with SOLiD and Illumina (>=1.3) reads.

Proper citation: SVDetect (RRID:SCR_010812) Copy   

•   Source: SciCrunch Registry

https://www.broadinstitute.org/scientific-community/science/programs/genome-sequencing-and-analysis/computational-rd/computational-

Software tool as whole genome shotgun assembler that can generate high quality genome assemblies using short reads (~100bp) such as those produced by the new generation of sequencers.

Proper citation: ALLPATHS-LG (RRID:SCR_010742) Copy   

•   Source: SciCrunch Registry

http://soap.genomics.org.cn/soapdenovo.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 24,2023. Software tool for de novo assembly of human genomes with massively parallel short read sequencing.Short-read assembly method that can build de novo draft assembly for human sized genomes.Software package for assembling short oligonucleotide into contigs and scaffolds., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SOAPdenovo (RRID:SCR_010752) Copy   

•   Source: SciCrunch Registry

https://www.hgsc.bcm.edu/content/atlas2

A next-generation sequencing suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in WECS data.

Proper citation: Atlas2 (RRID:SCR_010756) Copy   

•   Source: SciCrunch Registry

http://berry.engin.umich.edu/oligoarray2_1/

A free software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction.

Proper citation: OligoArray (RRID:SCR_010961) Copy   

•   Source: SciCrunch Registry

http://www.cbrc.kaust.edu.sa/hmcan/

A Hidden Markov Model based software tool that is developed to detect histone modification in cancer ChIP-seq data.

Proper citation: HMCan (RRID:SCR_010858) Copy   

•   Source: SciCrunch Registry

http://furlonglab.embl.de/methods/tools/coco

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 22, 2021.A computational tool that allows the user to search, visualise and store different data associated with gene expression.

Proper citation: CoCo (RRID:SCR_010947) Copy   

•   Source: SciCrunch Registry

http://liulab.dfci.harvard.edu/NPS/

A python software package that can identify nucleosome positions given histone-modification ChIP-seq or nucleosome sequencing at the nucleosome level.

Proper citation: NPS (RRID:SCR_010890) Copy   

•   Source: SciCrunch Registry

http://linus.nci.nih.gov/BRB-ArrayTools.html

An integrated software package for the visualization and statistical analysis of DNA microarray gene expression data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BRB-ArrayTools (RRID:SCR_010938) Copy   

•   Source: SciCrunch Registry

http://mmb.pcb.ub.es/nucleR/

A R/Bioconductor package for a flexible and fast recognition of nucleosome positioning from next generation sequencing and tiling arrays experiments. The software is integrated with standard high-throughput genomics R packages and allows for in situ visualization as well as to export results to common genome browser formats.

Proper citation: nucleR (RRID:SCR_010895) Copy   

•   Source: SciCrunch Registry

http://genovar.sourceforge.net/

A Detection and Visualization software tool for Genomic Variants.

Proper citation: Genovar (RRID:SCR_010930) Copy   

•   Source: SciCrunch Registry

http://bcb.dfci.harvard.edu/~gcyuan/MAnorm/MAnorm.htm

A robust software package for quantitative comparison of ChIP-Seq data sets.

Proper citation: MAnorm (RRID:SCR_010869) Copy   

•   Source: SciCrunch Registry

http://software.big.ac.cn/MeRIP-PF.html

A high-efficiency and easy-to-use analysis pipeline for MeRIP-Seq peak-finding at high resolution, which compares distributions of reads between immunoprecipitation sample and control sample.

Proper citation: MeRIP-PF (RRID:SCR_010904) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/batmeth/

Improved mapper for bisulfite sequencing reads on DNA methylation.

Proper citation: BatMeth (RRID:SCR_010906) Copy   

•   Source: SciCrunch Registry

http://quma.cdb.riken.jp/

You can easily align, visualize and quantify bisulfite sequence data for CpG methylation analysis.

Proper citation: QUMA (RRID:SCR_010907) Copy   

•   Source: SciCrunch Registry

http://ranger.sourceforge.net/

Software for a multi-purpose ChIP Seq peak caller.

Proper citation: PeakRanger (RRID:SCR_010863) Copy   

•   Source: SciCrunch Registry

http://biodoop-seal.sourceforge.net/

A suite of distributed software applications for aligning short DNA reads, and manipulating and analyzing short read alignments.

Proper citation: SEAL (RRID:SCR_010914) Copy   

•   Source: SciCrunch Registry