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http://mirexpress.mbc.nctu.edu.tw/
A stand-alone software package implemented for generating miRNA expression profiles from high-throughput sequencing of RNA without the need for sequenced genomes.
Proper citation: miRExpress (RRID:SCR_010831) Copy
An automated pipeline for detecting genetic variants from High-throUghput GEnome SEQuencing.
Proper citation: HugeSeq (RRID:SCR_010803) Copy
https://code.google.com/p/mutfinder/
It streamlines the next generation sequencing data analysis using BFAST for aligner, SAMTOOLS for SNP caller, and ANNOVAR for annotation.
Proper citation: MutFinder (RRID:SCR_010804) Copy
http://icbi.at/software/simplex/simplex.shtml
Cloud-enabled pipeline for the comprehensive analysis of exome sequencing data.
Proper citation: SIMPLEX (RRID:SCR_010807) Copy
http://epigen.hpc.cineca.it/wep/
A complete whole-exome sequencing pipeline and provides easy access through interface to intermediate and final results.
Proper citation: WEP (RRID:SCR_010809) Copy
http://compbio.cs.toronto.edu/modil/
Software for a novel method for finding medium sized indels from high throughput sequencing datasets.
Proper citation: MoDIL (RRID:SCR_010764) Copy
http://pgrc.ipk-gatersleben.de/misa/
Software tool that allows the identification and localization of perfect microsatellites as well as compound microsatellites which are interrupted by a certain number of bases.
Proper citation: MISA (RRID:SCR_010765) Copy
http://bioinfo.montp.cnrs.fr/?r=t-reks/
An algorithm for de novo detection and alignment of repeats in sequences based on K-means algorithm.
Proper citation: T-REKS (RRID:SCR_010768) Copy
http://www.phenosystems.com/www/index.php/products/gensearchngs
An integrated software solution for the analysis of DNA-Seq data from commonly used NGS equipments such as Roche/454, Illumina and Ion Torrent.
Proper citation: GensearchNGS (RRID:SCR_010802) Copy
http://www.insilicase.co.uk/agile/AgileVariantMapper.aspx
Software that visualises sequence variant data from whole exome data, so that it is possible to identify autozygous regions in consanguineous individuals.
Proper citation: AgileVariantMapper (RRID:SCR_010770) Copy
http://www.igbam.bilgem.tubitak.gov.tr/softwares/HomSI/
A software tool that identifies homozygous regions using deep sequence data.
Proper citation: HomSI (RRID:SCR_010771) Copy
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
http://cran.r-project.org/web/packages/ExomeCNV/index.html
A statistical method to detect CNV and LOH using depth-of-coverage and B-allele frequencies from mapped short sequence reads in exome sequencing data.
Proper citation: ExomeCNV (RRID:SCR_010815) Copy
http://www.precancer.leeds.ac.uk/software-and-datasets/cnanorm/
A Bioconductor package to estimate Copy Number Aberrations (CNA) in cancer samples.
Proper citation: CNAnorm (RRID:SCR_010816) Copy
https://code.google.com/p/cnvalidator/
Identifies high quality CNVs based on the density of homozygous SNPs and the ratio of heterozygous SNP reads.
Proper citation: CNValidator (RRID:SCR_010819) Copy
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
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
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
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