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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://www.nig.ac.jp/index-e.html

Institute for genetics, through National BioResource Project, collects, preserves, and provides bio-resources (strains, populations, tissues, cells, genes of animals, plants and microorganisms, and information on these materials for R&D use) that are essential for life science research.

Proper citation: National Institute of Genetics; Shizuoka; Japan (RRID:SCR_010836) Copy   

•   Source: SciCrunch Registry

http://rth.dk/resources/rnasnp/

Software / Web Server to predict the effect of SNPs on local RNA secondary structure based on the RNA folding algorithms implemented in the Vienna RNA package.

Proper citation: RNAsnp (RRID:SCR_010837) Copy   

•   Source: SciCrunch Registry

http://compgenomics.utsa.edu/gene/gene_1.php

A Bayesian decision fusion algorithm for microRNA target prediction that combines the prediction of TargetScan, miRanda, PicTar, mirTarget, PITA, and DianamicroT. Users enter a Ref_seq ID for a query target gene and select a miRNA, which BCmicrO will use in its predictive algorithm. The prediction results can then be downloaded.

Proper citation: BCmicrO (RRID:SCR_010838) 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

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   

•   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://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   

•   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/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   

•   Source: SciCrunch Registry