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http://metagenomics.atc.tcs.com/compression/DELIMINATE/
A practical implementation of a novel compression approach that can rapidly compress FASTA files containing genomic sequence data in a loss-less fashion.
Proper citation: DELIMINATE (RRID:SCR_008956) Copy
http://www.ics.uci.edu/~dnazip/
DNA sequence compression using a reference genome.
Proper citation: DNAzip (RRID:SCR_009032) Copy
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
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
http://hood.systemsbiology.net/rnaseqr.php
A streamlined and accurate RNA-seq sequence analysis program.
Proper citation: RNASEQR (RRID:SCR_009871) Copy
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
An application for discovering potential splice junctions in high throughput sequencing (HTS) data.
Proper citation: Supersplat (RRID:SCR_009826) Copy
http://soap.genomics.org.cn/soapsnp.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software providng a method based on Bayes? theorem (the reverse probability model) to call consensus genotype by carefully considering the data quality, alignment, and recurring experimental errors., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: SOAPsnp (RRID:SCR_010602) Copy
http://jr-assembler.iis.sinica.edu.tw/
An assembler for the de novo assembly of large genomes using short sequence reads via jumping extension and read remapping.
Proper citation: JR-Assembler (RRID:SCR_010681) Copy
http://cseweb.ucsd.edu/~ppevzner/software.html#EULER-short
Assembly package that contains a suite of software programs for correcting errors in short reads and assembling them. The assembler may take as input classical Sanger reads, 454 sequences, and Illumina reads.
Proper citation: EULER-SR (RRID:SCR_010485) Copy
http://www.genome.duke.edu/labs/ohler/research/MUMMIE/mir.html
Software for a specific model, implemented within the MUMMIE framework, for predicting micro-RNA binding sites using PAR-CLIP data.
Proper citation: MicroMUMMIE (RRID:SCR_010847) Copy
http://home.gwu.edu/~wpeng/Software.htm
A clustering software package for identification of enriched domains from histone modification ChIP-Seq data.
Proper citation: SICER (RRID:SCR_010843) Copy
http://www.netlab.uky.edu/p/bioinfo/MapSplice
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Accurate mapping of RNA-seq reads for splice junction discovery.
Proper citation: MapSplice (RRID:SCR_010844) Copy
http://sourceforge.net/p/mira-assembler/wiki/Home/
Sequence assembler and mapper for whole genome shotgun and EST/RNASeq sequencing data.
Proper citation: MIRA (RRID:SCR_010731) Copy
http://www.comp.nus.edu.sg/~bioinfo/peasm/PE_manual.htm
Software providing a method that eschews the traditional graph-based approach in favor of a simple 3'' extension approach that has potential to be massively parallelized.
Proper citation: PE-Assembler (RRID:SCR_010732) Copy
A quality-value guided de novo short read assembler.
Proper citation: QSRA (RRID:SCR_010733) Copy
http://compbio.med.harvard.edu/Supplements/BMCBioinfo10-2.html
Designed to identify CNVs between two genomes.
Proper citation: rSW-seq (RRID:SCR_010825) Copy
http://www.broadinstitute.org/software/cprg/?q=node/39
An algorithm to identify chromosomal breakpoints using massively parallel next generation sequence data.
Proper citation: SegSeq (RRID:SCR_010826) Copy
Offers the researchers an automatic pipeline to predict the disease-association of SAPs.
Proper citation: SAPRED (RRID:SCR_010785) Copy
http://seqanswers.com/wiki/JointSLM
Copy number estimation from read depth information.
Proper citation: JointSLM (RRID:SCR_010823) Copy
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