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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://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/p/mira-assembler/wiki/Home/

Sequence assembler and mapper for whole genome shotgun and EST/RNASeq sequencing data.

Proper citation: MIRA (RRID:SCR_010731) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/xdrawchem/

A drawing software application designed for drawing and analyzing chemical structures and reactions.

Proper citation: XDrawChem (RRID:SCR_010941) Copy   

•   Source: SciCrunch Registry

http://ppseq.sourceforge.net/

A software suite including a scalable hierarchical multitasking parallel infrastructure and the classical sequencing algorithms.

Proper citation: PPSEQ (RRID:SCR_010913) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/p/arpeggio/wiki/Home/

Software for harmonic compression of ChIP-seq data reveals protein-chromatin interaction signatures.

Proper citation: Arpeggio (RRID:SCR_010876) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/b-o-s-s/

Batch primer selection software program designed to select PCR oligos for gap closure for assemblies containing a large number of gaps. It will select oligos for gap closure of both contig and scaffold gaps.

Proper citation: Batch Oligo Selection Script (RRID:SCR_002808) Copy   

•   Source: SciCrunch Registry

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

A fast parallel error correction tool for short reads.

Proper citation: CUDA-EC (RRID:SCR_001090) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/qips/

A software package for analyzing ChIP-seq (Chromatin ImmunoPrecipitation on sequencing) data that finds enriched regions of arbitrary lengths and is therefore especially suited for analyzing ChIP-seq of histone marks or polymerase.

Proper citation: qips (RRID:SCR_001092) 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/cgap-align/

A time efficient read alignment tool built on the top of BWA.

Proper citation: CGAP-Align (RRID:SCR_000350) Copy   

•   Source: SciCrunch Registry