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http://sourceforge.net/projects/denovogear/

A software for detecting de novo mutations using sequencing data. It utilizes likelihood-based error modeling to reduce the false positive rate of mutative discovery in exome analysis. It also uses fragment information to identify the parental origin of germ-line mutations.

Proper citation: DeNovoGear (RRID:SCR_000670) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/srma/

A post-alignment micro re-aligner for next-generation high throughput sequencing data.

Proper citation: SRMA (RRID:SCR_000669) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/finesplice/

A software pipeline based on TopHat2 combined with a splice junction detection algorithm.

Proper citation: FineSplice (RRID:SCR_000691) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/particlecall/

A base-calling algorithm for Illumina DNA sequencing.

Proper citation: ParticleCall (RRID:SCR_001103) 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/dtailor/

A fully extendable software framework, for property-based design of synthetic DNA sequences.

Proper citation: D-Tailor (RRID:SCR_000115) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/sirnarules/

An open-source JAVA program that is surprisingly efficient at predicting active siRNAs.

Proper citation: siRNArules (RRID:SCR_000096) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/abmining/

Python scripts to analyze antibody libraries sequenced by next generation sequencing methods (454, Ion Torrent, MiSeq).

Proper citation: AbMining ToolBox (RRID:SCR_000090) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/spdesigner/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An open source software program for the design of specific PCR primer pairs from a DNA sequence alignment containing sequences from various taxa.

Proper citation: SP-Designer (RRID:SCR_000031) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mysirna/

Software that integrates several factors in an automated work-flow considering mRNA transcripts variations, siRNA and mRNA target accessibility, and both near-perfect and partial off-target matches.

Proper citation: MysiRNA-designer (RRID:SCR_000102) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/dprimer/

A command line software utility for designing degenerate PCR primers against multiple, aligned sequences. Its primary use case is searching for a family of related pathogens in a host tissue sample.

Proper citation: dprimer (RRID:SCR_000050) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/imethy/

Software for investigation and visualization of DNA methylation by high-throughput bisulfite sequencing.

Proper citation: iMethy (RRID:SCR_000049) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/protms/

A software tool for the proteomics community that may help improving analysis of proteomic experimental data.

Proper citation: Quant (RRID:SCR_000267) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/biogrinder/

An open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms. The tool is available through multiple interfaces like GUI, CLI and API. It is useful for simulating clinical or environmental microbial communities and complements the use of in vitro mock communities.

Proper citation: Grinder (RRID:SCR_000168) Copy   

•   Source: SciCrunch Registry

http://gprox.sourceforge.net/

A freely available complete software platform for comprehensive and integrated analysis and visualization of large proteomics datasets.

Proper citation: GProX (RRID:SCR_000273) Copy   

•   Source: SciCrunch Registry

http://peptideprophet.sourceforge.net/

Software that automatically validates peptide assignments to MS/MS spectra made by database search programs such as SEQUEST.

Proper citation: PeptideProphet (RRID:SCR_000274) Copy   

•   Source: SciCrunch Registry