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http://bio-bwa.sourceforge.net/

Software for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp.

Proper citation: BWA (RRID:SCR_010910) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/apps/mediawiki/cloudburst-bio/index.php?title=CloudBurst

A new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics.

Proper citation: CloudBurst (RRID:SCR_010911) Copy   

•   Source: SciCrunch Registry

http://erne.sourceforge.net/

A short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads.

Proper citation: ERNE (RRID:SCR_010912) Copy   

•   Source: SciCrunch Registry

http://fureylab.web.unc.edu/software/fseq/

A software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome Browser.

Proper citation: F-Seq (RRID:SCR_010880) Copy   

•   Source: SciCrunch Registry

http://homer.ucsd.edu/

Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++.

Proper citation: HOMER (RRID:SCR_010881) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/oncosnp/

An analytical software tool for characterizing copy number alterations and loss-of-heterozygosity (LOH) events in cancer samples from SNP genotyping data.

Proper citation: OncoSNP (RRID:SCR_012985) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/RLMM.html

A Genotype Calling Algorithm for Affymetrix SNP Arrays.

Proper citation: RLMM (RRID:SCR_012984) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ibdld/

A C++ software program for multipoint IBD estimation based on high density SNP genotype data.

Proper citation: IBDLD (RRID:SCR_013043) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/solsnp/

A Java-based DNA variant calling tool for Next-Generation Sequencing alignment data.

Proper citation: SolSNP (RRID:SCR_013045) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/tumorhats/

A software tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next generation sequencing tumor data.

Proper citation: HATS (RRID:SCR_013044) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/charm.html

Software package that implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol.

Proper citation: charm (RRID:SCR_012992) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/chipotle-perl/

A peak-finding algorithm used to analyze ChIP-chip microarray data.

Proper citation: ChIPOTle Peak Finder (RRID:SCR_012991) Copy   

•   Source: SciCrunch Registry

http://rnaseq-mats.sourceforge.net/

Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user defined threshold. Can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design.

Proper citation: Multivariate Analysis of Transcript Splicing (RRID:SCR_013049) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/BiSeq.html

Software package that provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data.

Proper citation: BiSeq (RRID:SCR_012993) Copy   

•   Source: SciCrunch Registry

http://trinityrnaseq.sourceforge.net/

Software for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.

Proper citation: Trinity (RRID:SCR_013048) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ngspeanalysis/

A pipeline using open-source tools which can implement a set of pair ended Next-generation sequencing analysis, include short reads alignment, high-quality variation genotype calling and variants annotation.

Proper citation: NGSpeAnalysis (RRID:SCR_013040) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/MEDME.html

Software that allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments.

Proper citation: MEDME (RRID:SCR_012995) Copy   

•   Source: SciCrunch Registry

https://github.com/brentp/methylcode

A single program that takes of bisulfite-treated reads and outputs per-base methylation data.

Proper citation: MethylCoder (RRID:SCR_012997) Copy   

•   Source: SciCrunch Registry

http://grassius.org/

A public resource composed of a collection of databases, computational and experimental resources that relate to the control of gene expression in the grasses, and their relationship with agronomic traits. As knowledge on the interactions of transcription factors (TFs) and cis-regulatory elements in the promoters of the genes that they regulate continues to accumulate, the information is acquired by GRASSIUS, either through contributions by the community, or by literature analysis. The overarching objective of GRASSIUS is to provide a one-stop resource that will facilitate research and communication within the plant community with regards to genome-wide regulation of gene expression processes.

Proper citation: GRASSIUS (RRID:SCR_012999) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/lofreq/

A fast and sensitive variant-caller for inferring single-nucleotide variants (SNVs) from high-throughput sequencing data.

Proper citation: LoFreq (RRID:SCR_013054) Copy   

•   Source: SciCrunch Registry