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http://sourceforge.net/projects/fitgcp/

Software providing a framework for fitting mixtures of probability distributions to genome coverage profiles.

Proper citation: fitGCP (RRID:SCR_006741) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/gasic/

A method to correct read alignment results for the ambiguities imposed by similarities of genomes.

Proper citation: GASiC (RRID:SCR_006765) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/atlas-link/

Software that implements a greedy algorithm and uses graph theory to link and orient assembled existing contigs quickly and accurately using mate pair information.

Proper citation: Next-gen Sequencing Scaffolding Tool (RRID:SCR_006762) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/quasr/

A lightweight software pipeline written to process and analyse next-generation sequencing (NGS) data from Illumina, 454, and Ion Torrent platforms. Although originally written for viral data, it is generic enough to work on any NGS dataset. Functions include: duplicate removal, demultiplexing, primer-removal, quality-assurance (QA) graphing, quality control (QC), consensus-generation, minority-variant determination, minority-variant graphing.

Proper citation: QUASR (RRID:SCR_006820) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/simhtsd/

Software that given a reference sequence, will create a large set of short nucleotide reads, simulating the output from today''s high-throughput DNA sequencers, such as the Illumina Genome Analyzer II.

Proper citation: simhtsd (RRID:SCR_006822) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/virmid/

A Java based variant caller designed for disease-control matched samples. Virmid is also specialized for identifying potential within individual contamination where the disease sample cannot be purified enough. While the SNP calling rate is severely compromised with this heterogeneity, Virmid can uncover SNPs with low allele frequency by considering the level of contamination (alpha). The important features of Virmid are: * Estimation of accurate proporation of control sample in a (mixed) disease sample * Improved SNP and somatic mutation calling with regard to the estimated proportion

Proper citation: Virmid (RRID:SCR_006780) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bigpre/

A quality assessment software package for next-genomics sequencing data.

Proper citation: BIGpre (RRID:SCR_006781) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/taxoassignement/

Software tool for the taxonomic assignment of Next Generation Sequencing reads using multiple reference taxonomy.

Proper citation: TaxoAssignement (RRID:SCR_006814) Copy   

•   Source: SciCrunch Registry

http://crossmap.sourceforge.net/

A software program for convenient conversion of genome coordinates (or annotation files) between different assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF. It is designed to liftover genome coordinates between assemblies. It?s not a program for aligning sequences to reference genome. CrossMap is not recommend for converting genome coordinates between species.

Proper citation: CrossMap (RRID:SCR_001173) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/apps/mediawiki/breakway/index.php

A suite of software programs that take aligned genomic data and report structural variation breakpoints. Features include: * Takes in BAM formatted input, the current standard for genomic alignments. * Compatible with standard output from major alignment algorithms such as BFAST, BWA, MAQ, et cetera. * Capable of analyzing data from any major platform--Solexa, SOLiD, 454, et cetera. * Empirically identifies structural variation breakpoints. * Highly specific analysis generates very few false positives. * Includes a suite of downstream tools for annotating identified breakpoints and reducing false positives.

Proper citation: Breakway (RRID:SCR_001180) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ngsrich/

Software for target enrichment performance for next-generation sequencing.

Proper citation: NGSrich (RRID:SCR_001333) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/pennseq/

Software for isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution. Instead of making parametric assumptions, they give adequate weight to the underlying data by the use of a non-parametric approach. The rationale is that regardless what factors lead to non-uniformity, whether it is due to hexamer priming bias, local sequence bias, positional bias, RNA degradation, mapping bias or other unknown reasons, the probability that a fragment is sampled from a particular region will be reflected in the aligned data. This empirical approach thus maximally reflects the true underlying non-uniform read distribution.

Proper citation: PennSeq (RRID:SCR_001763) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/pasha/

A parallel short read assembler for large genomes using de Bruijn graphs.

Proper citation: PASHA (RRID:SCR_004455) Copy   

•   Source: SciCrunch Registry

http://snoopcgh.sourceforge.net/

A java desktop application for visualising and exploring comparative genomic hybridization (CGH) data.

Proper citation: SnoopCGH (RRID:SCR_004420) Copy   

•   Source: SciCrunch Registry

https://computation-rnd.llnl.gov/lmat/

Open-source software tool to assign taxonomic labels to as many reads as possible in very large metagenomic datasets and report the taxonomic profile of the input sample. The quick "single pass" analysis of every read allows read binning to support additional more computationally expensive analysis such as metagenomic assembly or sensitive database searches on targeted subsets of reads.

Proper citation: LMAT (RRID:SCR_004646) Copy   

•   Source: SciCrunch Registry

http://useq.sourceforge.net/

A collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms.

Proper citation: USeq (RRID:SCR_004753) Copy   

•   Source: SciCrunch Registry

http://svmerge.sourceforge.net/

Software pipeline to detect structural variants (SVs) by integrating calls from several existing SV callers, which are then validated and the breakpoints refined using local de novo assembly. The output is in BED format allowing for easy downstream analysis or viewing in a genome browser. It is modular and extensible allowing new callers to be incorporated as they become available.

Proper citation: SVMerge (RRID:SCR_004777) Copy   

•   Source: SciCrunch Registry

http://petrov.stanford.edu/cgi-bin/Tlex.html

Software package for fast and accurate discovery, annotation, re-annotation and population analysis of Transposable Elements using Next-Generation Sequencing data.

Proper citation: T-lex (RRID:SCR_005134) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/gesnd/

A software package and a pipeline for identifying causal mutations for rare congenital diseases by next-generation sequencing. Features * one-stop solution for identifying causal mutations of rare genetic diseases * detect wide-spctrum variants, including medium and large sized indels, and tandem repeats * annotate and filter variants * prioritize candidate variants

Proper citation: GESND (RRID:SCR_005179) Copy   

•   Source: SciCrunch Registry

http://anntools.sourceforge.net/

Software tool for annotating single nucleotide substitutions (SNP/SNV), small insertions/deletions (indels), and copy number variations (CNV) calls generated from sequencing and microarray data. Only human genome build 37/hg19 can be annotated at this time.

Proper citation: AnnTools (RRID:SCR_005170) Copy   

•   Source: SciCrunch Registry