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http://microbiomeutil.sourceforge.net/#A_CS
A chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp).
Proper citation: ChimeraSlayer (RRID:SCR_013283) Copy
http://sourceforge.net/projects/telescoper/
An algorithm that iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework.
Proper citation: Telescoper (RRID:SCR_013206) Copy
http://sourceforge.net/projects/palfinder/
A perl script that finds microsatellite repeat elements directly from raw 454 or Illumina paired-end sequencing reads.
Proper citation: palfinder (RRID:SCR_013174) Copy
http://alumni.cs.ucr.edu/~liw/isolasso.html
An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.
Proper citation: IsoLasso (RRID:SCR_013176) Copy
http://sourceforge.net/projects/samcomp/
A simple arithmetic coding based compressor for the SAM and BAM (DNA sequence alignment) file format.
Proper citation: sam comp (RRID:SCR_013179) Copy
http://sourceforge.net/projects/heuraa/
Software for accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.
Proper citation: HeurAA (RRID:SCR_013212) Copy
http://sourceforge.net/projects/bisreadmapper/
Fast and lightweight package for mapping bisulfite converted DNA sequencing reads from the Illumina platform.
Proper citation: bisReadMapper (RRID:SCR_013171) Copy
http://www-rcf.usc.edu/~fsun/Programs/CEDER/CEDERmain.html
R package intended to implement a program for detecting differentially expressed genes (DEG) using RNA-Seq by combining significance of exons within a gene.
Proper citation: CEDER (RRID:SCR_013255) Copy
http://www-rcf.usc.edu/~liangche/software.html
A software tool to analyze RNA-seq data to estimate gene and exon expression, identify differentially expressed genes, and differentially spliced exons., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: GPSeq (RRID:SCR_013250) Copy
http://bioinfo.ctb.pku.edu.cn/MAP/
This resource is out of service. Documented on February 23,2021. Software for de novo metagenomic assembly program for shotgun DNA reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MAP (RRID:SCR_013216) Copy
http://www.netlab.uky.edu/p/bioinfo/DiffSplice
The Genome-Wide Detection of Differential Splicing Events with RNA-seq.
Proper citation: DiffSplice (RRID:SCR_013215) Copy
https://code.google.com/p/gencat/
Software designed as an open platform that allows users to incorporate as many datasets (concepts) as possible to annotate the input gene list, as long as these datasets are prepared in bigwig, BED, BAM/SAM formats.
Proper citation: genCAT (RRID:SCR_013220) Copy
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
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