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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
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
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
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
http://sourceforge.net/projects/samzip/
An encoding and decoding tool for Sequence Alignment/Map (SAM) files.
Proper citation: SAMZIP (RRID:SCR_012980) Copy
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
http://sourceforge.net/projects/shrec-ec/
A bioinformatics tool for error correction of HTS read data.
Proper citation: SHREC (RRID:SCR_013009) Copy
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
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
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
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
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
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
http://sourceforge.net/projects/conifer/
Uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes.
Proper citation: CoNIFER (RRID:SCR_013213) Copy
http://rdxplorer.sourceforge.net/
A computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage.
Proper citation: RDXplorer (RRID:SCR_013290) Copy
http://sourceforge.net/projects/pia2/
A prefix indexing and alignment software for next-generation sequencing (NGS) for whole human genome.
Proper citation: PIA (RRID:SCR_013267) Copy
A small tool for simulating sequence reads from a reference genome.
Proper citation: Wgsim (RRID:SCR_013269) Copy
http://soap.genomics.org.cn/SOAPdenovo-Trans.html
A de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: SOAPdenovo-Trans (RRID:SCR_013268) Copy
http://compbio.cs.ucr.edu/brat/
BRAT is an accurate and efficient tool for mapping short bisulfite-treated reads obtained from the Solexa-Illumina Genome Analyzer.
Proper citation: BRAT (RRID:SCR_013159) Copy
http://alumni.cs.ucr.edu/~liw/cem.html
An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.
Proper citation: CEM (RRID:SCR_013241) Copy
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