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http://bioinfo-out.curie.fr/projects/freec/tutorial.html

Prediction of copy number alterations and loss of heterozygosity using deep-sequencing data.

Proper citation: Control-FREEC (RRID:SCR_010822) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/readdepth/

This package for R can detect copy number aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome.

Proper citation: readDepth (RRID:SCR_010824) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/vibansal/software/hapcut

A max-cut based algorithm for haplotype assembly using sequence reads from the two chromosomes of an individual.

Proper citation: HapCUT (RRID:SCR_010791) Copy   

•   Source: SciCrunch Registry

http://www.popgen.dk/software/index.php/Relate

Software providing a method that estimates the probability of sharing alleles identity by descent (IBD) across the genome and can also be used for mapping disease loci using distantly related individuals.

Proper citation: Relate (RRID:SCR_010794) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://hugeseq.snyderlab.org/

An automated pipeline for detecting genetic variants from High-throUghput GEnome SEQuencing.

Proper citation: HugeSeq (RRID:SCR_010803) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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

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   

•   Source: SciCrunch Registry

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   

•   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

http://snps.biofold.org/phd-snp/phd-snp.html

It is based a SVM-based classifier.

Proper citation: PhD-SNP (RRID:SCR_010782) Copy   

•   Source: SciCrunch Registry