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    • RRID:SCR_012979

http://sourceforge.net/projects/quicktsaf/

Tool that compresses and decompresses fastq files.

Proper citation: KungFq (RRID:SCR_012979) Copy   

    • RRID:SCR_013031

    This resource has 1+ mentions.

http://sourceforge.net/projects/ncproseq/

Software that aims to interrogate and perform detailed analysis on small RNAs derived from annotated non-coding regions.

Proper citation: ncPRO-seq (RRID:SCR_013031) Copy   

    • RRID:SCR_013034

http://sourceforge.net/projects/vcf2msat/

A python software program to identify microsatellite repeat regions based on known polymorphisms identified in a .vcf report after using SAMtools to analyze next-generation sequencing files.

Proper citation: vcf2MSAT (RRID:SCR_013034) Copy   

    • RRID:SCR_013038

    This resource has 10+ mentions.

http://sourceforge.net/projects/fishingcnv/

A software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data.

Proper citation: FishingCNV (RRID:SCR_013038) Copy   

    • RRID:SCR_012982

    This resource has 10+ mentions.

http://sourceforge.net/projects/msaprobs/

An open-source protein multiple sequence ailgnment algorithm, achieving the stastistically highest alignment accuracy on popular benchmarks.

Proper citation: MSAProbs (RRID:SCR_012982) Copy   

    • RRID:SCR_013002

    This resource has 1+ mentions.

http://sourceforge.net/projects/qcreads/

Provides an efficient tool for trimming adapter sequences and low quality sequences, in raw reads generated by the high throughput sequencing platforms.

Proper citation: QcReads (RRID:SCR_013002) Copy   

    • RRID:SCR_013082

    This resource has 100+ mentions.

https://bitbucket.org/nsegata/phylophlan/wiki/Home

Software pipeline for reconstructing highly accurate and resolved phylogenetic trees based on whole-genome sequence information. Pipeline is scalable to thousands of genomes and uses the most conserved 400 proteins for extracting the phylogenetic signal. PhyloPhlAn also implements taxonomic curation, estimation, and insertion operations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PhyloPhlAn (RRID:SCR_013082) Copy   

    • RRID:SCR_013007

    This resource has 50+ mentions.

http://sourceforge.net/projects/hector454/

A parallel multistage k-hopo spectrum based homopolymer-length error corrector for 454 sequencing data.

Proper citation: HECTOR (RRID:SCR_013007) Copy   

    • RRID:SCR_013011

    This resource has 10+ mentions.

http://www.bioconductor.org/packages/2.12/bioc/html/BayesPeak.html

Software package that is an implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data.

Proper citation: BayesPeak (RRID:SCR_013011) Copy   

    • RRID:SCR_013016

http://www.bioconductor.org/packages/2.12/bioc/html/ChIPseqR.html

Software that identifies protein binding sites from ChIP-seq and nucleosome positioning experiments.

Proper citation: ChIPseqR (RRID:SCR_013016) Copy   

    • RRID:SCR_012960

    This resource has 10+ mentions.

http://sourceforge.net/projects/mirdeepstar/

An integrated application software tool for miRNA identification from RNA sequencing data.

Proper citation: miRDeep* (RRID:SCR_012960) Copy   

    • RRID:SCR_013065

    This resource has 1+ mentions.

http://www.genomic.ch/edena.php

Software providing a method that automatically determines suited overlaps cutoffs according to the contextual coverage, reducing thus the need for manual parameterization.

Proper citation: Edena v3 (RRID:SCR_013065) Copy   

    • RRID:SCR_013066

    This resource has 1+ mentions.

http://sourceforge.net/projects/contrail-bio/

A Hadoop based genome assembler for assembling large genomes in the clouds.

Proper citation: Contrail (RRID:SCR_013066) Copy   

    • RRID:SCR_013068

    This resource has 1+ mentions.

http://code.google.com/p/ngopt/wiki/A5PipelineREADME

A pipeline for assembling DNA sequence data generated on the Illumina sequencing platform.

Proper citation: A5 (RRID:SCR_013068) Copy   

    • RRID:SCR_013075

    This resource has 10+ mentions.

http://aluru-sun.ece.iastate.edu/doku.php?id=reptile

A software developed in C++ for correcting sequencing errors in short reads from next-gen sequencing platforms.

Proper citation: Reptile (RRID:SCR_013075) Copy   

    • RRID:SCR_009972

    This resource has 1+ mentions.

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   

    • RRID:SCR_009910

http://kks.inf.kcl.ac.uk/MSbind.html

Software tool that calculates features of meta-stable RNA secondary structure target sites.

Proper citation: MSbind (RRID:SCR_009910) Copy   

    • RRID:SCR_009871

http://hood.systemsbiology.net/rnaseqr.php

A streamlined and accurate RNA-seq sequence analysis program.

Proper citation: RNASEQR (RRID:SCR_009871) Copy   

    • RRID:SCR_009809

    This resource has 1+ mentions.

http://www.ufrgs.br/RNAi/isomiRID/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on 4/1/14. Software providing a framework to find isomiRNAs, templated and non-templated modifications in microRNAs.

Proper citation: isomiRID (RRID:SCR_009809) Copy   

    • RRID:SCR_009826

    This resource has 1+ mentions.

http://mocklerlab.org/tools/1

An application for discovering potential splice junctions in high throughput sequencing (HTS) data.

Proper citation: Supersplat (RRID:SCR_009826) Copy   

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