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http://snpeff.sourceforge.net/

Genetic variant annotation and effect prediction software toolbox that annotates and predicts effects of variants on genes (such as amino acid changes). By using standards, such as VCF, SnpEff makes it easy to integrate with other programs.

Proper citation: SnpEff (RRID:SCR_005191) Copy   

•   Source: SciCrunch Registry

http://ingap.sourceforge.net/

Software mining pipeline guided by a Bayesian principle to detect single nucleotide polymorphisms, insertion and deletions by comparing high-throughput pyrosequencing reads with a reference genome of related organisms. This pipeline is extended to identify and visualize large-size structural variations, including insertions, deletions, inversions and translocations.

Proper citation: inGAP (RRID:SCR_005261) Copy   

•   Source: SciCrunch Registry

http://covcal.sourceforge.net/

Small and very fast utility to calculate X-coverage from Next-Generation-Sequencing data.

Proper citation: CoverageCalculator (RRID:SCR_005352) Copy   

•   Source: SciCrunch Registry

http://mrfast.sourceforge.net/

Software designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient mannerl. Currently Supported Features: * Output in SAM format * Indels up to 8 bp (4 bp deletions and 4 bp insertions) * Paired-end mapping ** Discordant option to generate mapping file ready for VariationHunter to detect structural variants. * One end anchored (OEA) map locations for novel sequence insertion detection with NovelSeq * Matepair library mapping (long inserts with RF orientation). Planned Features: * Multithreading

Proper citation: mrFAST (RRID:SCR_005487) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/cushaw2/files/CUSHAW2-GPU/

Software program (based on CUSHAW2) designed and optimized for Kepler-based GPUs, but still workable on earlier-generation Fermi-based ones.

Proper citation: CUSHAW2-GPU (RRID:SCR_005480) Copy   

•   Source: SciCrunch Registry

http://cushaw2.sourceforge.net/homepage.htm#latest

Software package for next-generation sequencing read alignment that is fast and parallel gapped read alignment to large genomes, such as the human genome.

Proper citation: CUSHAW (RRID:SCR_005479) Copy   

•   Source: SciCrunch Registry

http://cliiq.sourceforge.net/Home

An algorithm to simultaneously identify and quantify expressed isoforms based on RNA-Seq data from multiple sample(s) in a population.

Proper citation: CLIIQ (RRID:SCR_009972) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mirdeepstar/

An integrated application software tool for miRNA identification from RNA sequencing data.

Proper citation: miRDeep* (RRID:SCR_012960) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/trowel-ec/

An error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach.

Proper citation: Trowel (RRID:SCR_012890) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/oncosts/

Software for a web-based Laboratory Information Management System for sample and analysis tracking in oncogenomic experiments.

Proper citation: Onco-STS (RRID:SCR_012990) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/nxgview/

A virtual software pipeline that contains several PERL modules for processing next generation sequencing data.

Proper citation: NxGview (RRID:SCR_012994) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bamformatics/

Software that provides a coherent and consistent approach to analysis of high-throughput sequencing data.

Proper citation: Bamformatics (RRID:SCR_013041) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bsmapper/

Sequence mapper for bisulfite sequencing reads for DNA methylation studies.

Proper citation: BSmapper (RRID:SCR_012998) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mendelscan/

A software tool for prioritizing candidate variants in family-based studies of inherited disease.

Proper citation: MendelScan (RRID:SCR_013053) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/probeselect/

Software for selecting probes in heterogenous transcriptional sets.

Proper citation: ProbeSelect (RRID:SCR_012965) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/seqgenomebrowse/

Mini cross-platform local genome browser software designed for visualizing next-generation sequencing data.

Proper citation: SeqGenome Browser (RRID:SCR_012970) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mirdp/

A computational tool for analyzing the microRNA (miRNA) transcriptome in plants.

Proper citation: miRDeep-P (RRID:SCR_013026) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/quicktsaf/

Tool that compresses and decompresses fastq files.

Proper citation: KungFq (RRID:SCR_012979) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ncproseq/

Software that aims to interrogate and perform detailed analysis on small RNAs derived from annotated non-coding regions.

Proper citation: ncPRO-seq (RRID:SCR_013031) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/vcf2msat/

A python software program to identify microsatellite repeat regions based on known polymorphisms identified in a .vcf report after using SAMtools to analyze next-generation sequencing files.

Proper citation: vcf2MSAT (RRID:SCR_013034) Copy   

•   Source: SciCrunch Registry