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http://sourceforge.net/projects/socs/
Performs ungapped alignment of SOLiD (color space) sequencing reads against reference sequences.
Proper citation: SOCS (RRID:SCR_013223) Copy
http://www.bioconductor.org/packages//2.10/bioc/html/aCGH.html
Software functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects.
Proper citation: aCGH (RRID:SCR_013232) Copy
http://sourceforge.net/projects/denovosolid/
Pipeline for small genome assembly using SOLiD sequencing technology.
Proper citation: DSP (RRID:SCR_013114) Copy
https://github.com/adaptivegenome/repeatseq
Software that determines genotypes for microsatellite repeats in high-throughput sequencing data.
Proper citation: RepeatSeq (RRID:SCR_013235) Copy
http://sourceforge.net/projects/tuxe/
Software that manages the RNA-sequencing pipeline based on the TopHat suite of software automatically.
Proper citation: Tuxedo (RRID:SCR_013194) Copy
http://www.seqan.de/projects/microrazers/
A software tool optimized for mapping short RNAs onto a reference genome.
Proper citation: MicroRazerS (RRID:SCR_013316) Copy
http://archive.gersteinlab.org/proj/rnaseq/fusionseq/
A modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data.
Proper citation: FusionSeq (RRID:SCR_013329) Copy
http://seqtracs.sourceforge.net/
Software for a Laboratory Information Management System (LIMS) for tracking, organizing, and accessing sequencing requests and ABI trace files produced by a centralized sequencing core facility.
Proper citation: SeqTRACS (RRID:SCR_013294) Copy
http://tomcatbackup.esat.kuleuven.be/inclusive/
A suit of algorithms and tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements.
Proper citation: INCLUSive (RRID:SCR_013488) Copy
http://ctb.pku.edu.cn/main/SheGroup/Software/MED2.htm
A non-supervised gene prediction algorithm for prokaryotic genomes with multivariate entropy distance method.
Proper citation: MED (RRID:SCR_013403) Copy
http://hannonlab.cshl.edu/Alta-Cyclic/main.html
An Illumina Genome-Analyzer (Solexa) base caller.
Proper citation: Alta-Cyclic (RRID:SCR_013373) 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://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
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