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http://sourceforge.net/projects/asoovir/

A set of Ruby modules to annotate consequence terms, defined by the Sequence Ontology, of variants (SNP/SNVs, INDELs, SVs, CNAs) using Ensembl gene sets. Prior to annotation of variants an Ensembl gene set and reference coding sequences are loaded into memory from a database file, which can be downloaded or generated by the user from reference files. This allows rapid annotation of variants, making it suitable for annotation of whole genome scale calls. Annotation is performed on a transcript level basis, identifying associated sequence ontology terms for affected and nearby transcripts. Default output can be obtained on a gene basis, summarising the consequences for each gene affected, or on a transcript level basis. Output information is also readily customisable using user-generated scripts.

Proper citation: ASOoViR (RRID:SCR_005161) Copy   

•   Source: SciCrunch Registry

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://ngsview.sourceforge.net/

A generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface.

Proper citation: NGSView (RRID:SCR_005637) Copy   

•   Source: SciCrunch Registry

http://samtools.sourceforge.net/tview.shtml

Text alignment viewer software based on the GNU ncurses library that works with short indels and shows MAQ consensus. It uses different colors to display mapping quality or base quality, subjected to users' choice.

Proper citation: SAMtools Text Alignment Viewer (RRID:SCR_005611) Copy   

•   Source: SciCrunch Registry

http://manatee.sourceforge.net/

Manatee is a web-based gene evaluation and genome annotation tool; Manatee can store and view annotation for prokaryotic and eukaryotic genomes. The Manatee interface allows biologists to quickly identify genes and make high quality functional assignments, such as GO classifications, using search data, paralogous families, and annotation suggestions generated from automated analysis. Manatee can be downloaded and installed to run under the CGI area of a web server, such as Apache. Platform: Online tool, Linux compatible, Solaris

Proper citation: Manatee (RRID:SCR_005685) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/cancergrid-tma/

A web-based application for the management and storage of tissue microarray (TMA) images and the associated metadata. The application enables the user to navigate a grid of TMA core images within a slide, zoom and pan around an image, and enter a score constrained to a specific scoring system. The submitted scores are scored in the eXist open source database, in an XML format, which is compatible with existing TMA standards, and thus allow the data to be archived and re-used in future analysis.

Proper citation: cancergrid-tma (RRID:SCR_005595) Copy   

•   Source: SciCrunch Registry

http://ebardenovo.sourceforge.net/

Highly accurate de novo assembly of RNA-Seq with efficient chimera-detection.

Proper citation: EBARDenovo (RRID:SCR_011890) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/apps/mediawiki/seqgene/?title=SeqGene

An open-source software for mining next-gen sequencing datasets, focusing on post-alignment quality control, SNP and indel identification and annotation, RNA expression quantification, etc.

Proper citation: SeqGene (RRID:SCR_011861) Copy   

•   Source: SciCrunch Registry

http://bayescall.sourceforge.net/

An efficient model-based base-calling algorithm for high-throughput sequencing.

Proper citation: naiveBayesCall (RRID:SCR_011866) Copy   

•   Source: SciCrunch Registry

http://scalpel.sourceforge.net/

A software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology (e.g., Illumina).

Proper citation: Scalpel (RRID:SCR_012107) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/snpratiotest/

Software to calculate the number of significant SNPs in pathway divided by the number of SNPs in pathway.

Proper citation: SNP ratio test (RRID:SCR_012070) Copy   

•   Source: SciCrunch Registry

http://toxtree.sourceforge.net/

A full-featured and flexible user-friendly open source software application, which is able to estimate toxic hazard by applying a decision tree approach.

Proper citation: Toxtree (RRID:SCR_012086) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/viewmol/

Software providing a graphical front end for computational chemistry programs.

Proper citation: Viewmol (RRID:SCR_012088) Copy   

•   Source: SciCrunch Registry

http://toxmatch.sourceforge.net/

A software tool to facilitate chemical similarity calculations.

Proper citation: Toxmatch (RRID:SCR_012087) Copy   

•   Source: SciCrunch Registry

http://qutemol.sourceforge.net/

Open source (GPL) software providing an interactive, high quality molecular visualization system.

Proper citation: QuteMol (RRID:SCR_012089) Copy   

•   Source: SciCrunch Registry