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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
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
A tool to predict whether a nonsynonymous single nucleotide polymorphism (nsSNP) has a phenotypic effect.
Proper citation: nsSNPAnalyzer (RRID:SCR_010780) Copy
http://snps.biofold.org/phd-snp/phd-snp.html
It is based a SVM-based classifier.
Proper citation: PhD-SNP (RRID:SCR_010782) Copy
A software aimed at the annotation and prediction of pathological mutations.
Proper citation: PMut (RRID:SCR_010783) Copy
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
http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Main_Page
A de novo whole-genome shotgun (WGS) DNA sequence assembler.
Proper citation: Celera assembler (RRID:SCR_010750) Copy
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
http://bioinformatics.nyu.edu/wordpress/projects/sutta/
A new De Novo DNA sequence assembler based on global search-methods in order to contain the complexity of the assembly problem.
Proper citation: SUTTA (RRID:SCR_010754) Copy
http://www.molecularevolution.org/software/genomics/velvet
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package as de novo genomic assembler for short read sequencing technologies using de Bruijn graphs. Takes in short read sequences, removes errors, then produces high quality unique contigs, retrieves repeated areas between contigs. Can leverage very short reads in combination with read pairs to produce useful assemblies. Operating system Unix/Linux., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Velvet (RRID:SCR_010755) Copy
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
http://odin.mdacc.tmc.edu/~wwang7/FamSeqIndex.html
A computational tool for calculating probability of variants in family-based sequencing data.
Proper citation: FamSeq (RRID:SCR_010760) Copy
http://ribopicker.sourceforge.net/
Software to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets.
Proper citation: riboPicker (RRID:SCR_000360) Copy
A software for genome assembly, and is specifically designed to analyze long Sanger-chemistry reads.
Proper citation: ARACHNE (RRID:SCR_000351) Copy
http://parsecnv.sourceforge.net/
Software that takes CNV calls as input and creates SNP based statistics for CNV occurrence in cases and controls then calls CNVRs based on neighboring SNPs of similar significance.
Proper citation: ParseCNV (RRID:SCR_000355) Copy
http://sourceforge.net/projects/kinannote/
Software that identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine / threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com.
Proper citation: Kinannote (RRID:SCR_000352) Copy
http://sourceforge.net/projects/jnomics/
A collection of cloud-scale DNA sequence analysis tools.
Proper citation: Jnomics (RRID:SCR_000348) Copy
A genome browser framework which gives an open browsing experience, open data access, collaborative work support, and a framework to import annotations. Multiple data access approaches are supported for external platforms to retrieve data from ABrowse. This resource also contains an online user-space in which users can create, store and share comments, annotations and landmarks.
Proper citation: ABrowse (RRID:SCR_000345) Copy
http://icbi.at/software/gpviz/gpviz.shtml
A versatile Java-based software used for dynamic gene-centered visualization of genomic regions and/or variants.
Proper citation: GPViz (RRID:SCR_000346) Copy
http://www.bioconductor.org/packages/release/bioc/html/iASeq.html
Software that uses a Bayesian hierarchical mixture model to learn correlation patterns of allele-specificity among multiple proteins.
Proper citation: iASeq (RRID:SCR_000420) Copy
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