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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   

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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   

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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   

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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   

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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://solexaqa.sourceforge.net/

Software package to calculate sequence quality statistics and create visual representations of data quality for Illumina's second-generation sequencing technology.

Proper citation: SolexaQA (RRID:SCR_005421) 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://sybil.sourceforge.net/

A web-based software package for comparative genomics.

Proper citation: Sybil (RRID:SCR_005593) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/dna-bison/

Allows users with access to a computer cluster to rapidly align whole-genome bisulfite sequencing or RRBS reads.

Proper citation: dna-bison (RRID:SCR_005913) Copy   

•   Source: SciCrunch Registry
  

http://jmol.sourceforge.net/

An open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems and features an applet, application, and systems integration component.

Proper citation: Jmol (RRID:SCR_003796) Copy   

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http://sourceforge.net/projects/insertionmapper/

A pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. It consists of four independently working modules: Data Preprocessing, Database Modeling, Dimension Deconvolution and Element Mapping. This pipeline tool is applicable to scenarios requiring analysis of the tremendous output of short reads produced in NGS sequencing experiments of targeted genome sequences.

Proper citation: InsertionMapper (RRID:SCR_004163) Copy   

•   Source: SciCrunch Registry
  

http://cb-commander.sourceforge.net/pmwiki.php

A plugin based software tool that tries to integrate high throughput sequencing algorithms. It allows researchers to design and execute their experiments through a user friendly interface, enabling users to integrate di erent components of an experiment, e.g. algorithms and converters, into one graphically interfaced application that is very easy to use when working on remote servers as well as local computers. The graphical user interface facilitates a visual design of experiments by using a block diagram to represent the components (algorithms, converters, etc.) of an experiment as a pipeline. The users can easily modify this pipeline.

Proper citation: CB-Commander (RRID:SCR_004237) 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   

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http://mged.sourceforge.net/ontologies/MGEDontology.php

An ontology including concepts, definitions, terms, and resources for a standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1. These terms will enable structure queries of elements of the experiments. Furthermore, the terms will also enable unambiguous descriptions of how the experiment was performed.

Proper citation: MGED Ontology (RRID:SCR_004484) 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