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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

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    • RRID:SCR_013018

    This resource has 50+ mentions.

http://sourceforge.net/projects/swiftng/

An open source package for primary data analysis on next-gen sequence data from images to basecalls. Currently Swift is targeted toward Solexa/Illumina sequencing, but is designed to be platform agnostic.

Proper citation: Swift (RRID:SCR_013018) Copy   

    • RRID:SCR_012962

    This resource has 1+ mentions.

http://sourceforge.net/projects/cloudaligner/

A map/reduce based application for mapping short reads generated by the next-generation sequencing machines.

Proper citation: CloudAligner (RRID:SCR_012962) Copy   

    • RRID:SCR_013017

    This resource has 1+ mentions.

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

Software that provides probabilistic base calling, quality checks and diagnostic plots for Solexa sequencing data.

Proper citation: Rolexa (RRID:SCR_013017) Copy   

    • RRID:SCR_012964

    This resource has 10+ mentions.

http://www.ra.cs.uni-tuebingen.de/software/InCroMAP/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5,2023. Integrated analysis of cross-platform microarray and pathway data.

Proper citation: InCroMAP (RRID:SCR_012964) Copy   

    • RRID:SCR_013019

    This resource has 10+ mentions.

http://sourceforge.net/projects/tracetuner/

Software tool for base and quality calling of trace files from DNA sequencing instruments.

Proper citation: TraceTuner (RRID:SCR_013019) Copy   

    • RRID:SCR_013020

    This resource has 100+ mentions.

http://sourceforge.net/projects/seqminer/

Software for a genome wide mapping data interpretation platform for NGS (ChIPSeq).

Proper citation: seqMINER (RRID:SCR_013020) Copy   

    • RRID:SCR_013025

    This resource has 100+ mentions.

http://sourceforge.net/projects/mireap/

A software tool which can be used to identify both known and novel microRNAs from small RNA libraries deeply sequenced by Solexa/454/Solid technology.

Proper citation: MIREAP (RRID:SCR_013025) Copy   

    • RRID:SCR_013024

    This resource has 1+ mentions.

http://www.lgm.upmc.fr/mirena/index.html

A software tool to find microRNAs with high accuracy and no learning at genome scale and from deep sequencing data.

Proper citation: MIReNA (RRID:SCR_013024) Copy   

    • RRID:SCR_012972

    This resource has 1+ mentions.

https://mig.molbiol.ox.ac.uk/mig/

Allows the user to conveniently compare data from many loci., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MIG (RRID:SCR_012972) Copy   

    • RRID:SCR_012981

    This resource has 10+ mentions.

http://sourceforge.net/projects/msa-edna/

Software for Multiple Sequence Alignment for Transcription Factor Binding Sites using Di nucleotides dependencies and relying on Free Interaction energies between neighbouring DNA bases to stabilise substitution energy of the alignment.

Proper citation: EDNA (RRID:SCR_012981) Copy   

    • RRID:SCR_013036

    This resource has 10+ mentions.

http://bioconductor.org/packages/2.12/bioc/html/cn.mops.html

A data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data.

Proper citation: cn.mops (RRID:SCR_013036) Copy   

    • RRID:SCR_012980

http://sourceforge.net/projects/samzip/

An encoding and decoding tool for Sequence Alignment/Map (SAM) files.

Proper citation: SAMZIP (RRID:SCR_012980) Copy   

    • RRID:SCR_013037

    This resource has 10+ mentions.

http://sammate.sourceforge.net/

An open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate.

Proper citation: SAMMate (RRID:SCR_013037) Copy   

    • RRID:SCR_013009

    This resource has 10+ mentions.

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

A bioinformatics tool for error correction of HTS read data.

Proper citation: SHREC (RRID:SCR_013009) Copy   

    • RRID:SCR_013010

http://sourceforge.net/projects/hictools/

This collection of tools stream-lines the processing of HiC data from raw sequence to contact matrices and beyond.

Proper citation: hiCtools (RRID:SCR_013010) Copy   

    • RRID:SCR_013064

    This resource has 1+ mentions.

http://sourceforge.net/projects/locas/

A software to assemble short reads of next generation sequencing technologies at low coverage.

Proper citation: LOCAS (RRID:SCR_013064) Copy   

    • RRID:SCR_013069

    This resource has 1+ mentions.

http://sourceforge.net/projects/vdjfasta/?source=navbar

Bioinformatics Perl extension for the analysis of antibody variable domain repertoires.

Proper citation: VDJFasta (RRID:SCR_013069) Copy   

    • RRID:SCR_013060

    This resource has 1+ mentions.

http://sourceforge.net/projects/vcake/

A genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error.

Proper citation: VCAKE (RRID:SCR_013060) Copy   

    • RRID:SCR_013063

    This resource has 100+ mentions.

http://derisilab.ucsf.edu/software/price/index.html

Software for a de novo genome assembler implemented in C++.

Proper citation: PRICE (RRID:SCR_013063) Copy   

    • RRID:SCR_013175

    This resource has 50+ mentions.

http://www.bioconductor.org/packages//2.10/bioc/html/HiTC.html

Software package to explore high-throughput ''C'' data such as 5C or Hi-C.

Proper citation: HiTC (RRID:SCR_013175) Copy   

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