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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
https://confluence.crbs.ucsd.edu/display/NIF/OntoQuestMain
An ontology management module to perform ontology-based search over data sources. This management system permits a user to store, search and navigate any number of OWL-structured ontologies. Ontoquest may also be accessed through a variety of web services via the Neuroscience Information Framework.
Proper citation: OntoQuest (RRID:SCR_013281) 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://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
Software for a normalization scheme that corrects nucleotide composition bias, mappability variations and differential local DNA structural effects in deep sequencing data.
Proper citation: BEADS (RRID:SCR_013229) Copy
http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss
A software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data.
Proper citation: Trans-ABySS (RRID:SCR_013322) Copy
http://code.google.com/p/chimerascan/
Software package that detects gene fusions in paired-end RNA sequencing (RNA-Seq) datasets. Used for detection of chimeric transcripts in high-throughput sequencing data.
Proper citation: chimerascan (RRID:SCR_013298) Copy
http://bioinfo.au.tsinghua.edu.cn/software/pcs/
A stand-alone package to identify and analyze conserved k-mers in pairwise alignment. This program shows high performance for identifying miRNA seed binding sites in 3''-UTRs.
Proper citation: Pairwise Conservation Scores - An Algorithm to Identify Conserved K-mers (RRID:SCR_013409) Copy
http://www.eisenlab.org/eisen/?page_id=42
Software to graphically browse results of clustering and other analyses from Cluster.
Proper citation: TreeView (RRID:SCR_013503) Copy
http://tiger.dbs.nus.edu.sg/cnv-seq/
A method for detecting DNA copy number variation (CNV) using high-throughput sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CNV-seq (RRID:SCR_013357) Copy
https://dogma.ccbb.utexas.edu/
Web-based annotation tool for plant chloroplasts and animal mitochondrial genomes. DOGMA allows the use of BLAST searches against a custom database, and conservation of basepairing in the secondary structure of animal mitochondrial tRNAs to identify and annotate genes.
Proper citation: DOGMA (RRID:SCR_015060) Copy
http://floresta.eead.csic.es/primers4clades
Web application for the design of PCR primers for cross-species amplification of novel sequences from metagenomic DNA or from uncharacterized organisms belonging to user-specified phylogenetic lineages. It implements an extended CODEHOP strategy and evaluates thermodynamic properties of the oligonucleotide pairs.
Proper citation: primers4clades (RRID:SCR_015714) Copy
http://www.genome.umd.edu/masurca.html
A whole genome assembly software that combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MaSuRCA (RRID:SCR_010691) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Integrated RNA-Seq read analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CRAC (RRID:SCR_010652) Copy
http://compbio.cs.toronto.edu/CNVer/
A method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation.
Proper citation: CNVer (RRID:SCR_010820) Copy
http://www.popgen.dk/software/index.php/Relate
Software providing a method that estimates the probability of sharing alleles identity by descent (IBD) across the genome and can also be used for mapping disease loci using distantly related individuals.
Proper citation: Relate (RRID:SCR_010794) Copy
http://compbio.cs.toronto.edu/modil/
Software for a novel method for finding medium sized indels from high throughput sequencing datasets.
Proper citation: MoDIL (RRID:SCR_010764) Copy
http://pgrc.ipk-gatersleben.de/misa/
Software tool that allows the identification and localization of perfect microsatellites as well as compound microsatellites which are interrupted by a certain number of bases.
Proper citation: MISA (RRID:SCR_010765) Copy
http://www.phenosystems.com/www/index.php/products/gensearchngs
An integrated software solution for the analysis of DNA-Seq data from commonly used NGS equipments such as Roche/454, Illumina and Ion Torrent.
Proper citation: GensearchNGS (RRID:SCR_010802) Copy
http://www.igbam.bilgem.tubitak.gov.tr/softwares/HomSI/
A software tool that identifies homozygous regions using deep sequence data.
Proper citation: HomSI (RRID:SCR_010771) Copy
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