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http://www.ebi.ac.uk/~zerbino/oases/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool as de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.
Proper citation: Oases (RRID:SCR_011896) Copy
https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/rnnotator
Software designed to assemble Illumina single or paired-end reads.
Proper citation: Rnnotator (RRID:SCR_011897) Copy
http://genome.cshlp.org/content/20/10/1432.full
A de novo transcriptome assembly from next-generation sequencing data.
Proper citation: STM (RRID:SCR_011898) Copy
http://tophat.cbcb.umd.edu/fusion_index.html
An algorithm for Discovery of Novel Fusion Transcripts with the ability to align reads across fusion points, which results from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome.
Proper citation: TopHat-Fusion (RRID:SCR_011899) Copy
http://www.cbcb.umd.edu/software/glimmer-mg/
A software system for finding genes in environmental shotgun DNA sequences.
Proper citation: Glimmer-MG (RRID:SCR_011932) Copy
http://whale.bio.titech.ac.jp/metagene/
A gene-finding software program for prokaryote and phage., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MetaGeneAnnotator (RRID:SCR_011934) Copy
http://www.cse.sc.edu/~elallali/research/MGC.html
A software application for finding complete and incomplete genes in metagenomic reads.
Proper citation: MGC (RRID:SCR_011935) Copy
http://ab.inf.uni-tuebingen.de/software/metasim/
A Sequencing Simulator for Genomics and Metagenomics.
Proper citation: MetaSim (RRID:SCR_011940) Copy
http://ab.inf.uni-tuebingen.de/software/megan/
Software for analyzing metagenomes.
Proper citation: MEGAN (RRID:SCR_011942) Copy
http://vm-lux.embl.de/~kultima/MOCAT//
Software package for analyzing metagenomics datasets.
Proper citation: MOCAT (RRID:SCR_011943) Copy
A clustering algorithm focusing on noise injection for subsequent cluster validation.
Proper citation: pyGCluster (RRID:SCR_011944) Copy
http://artiva.gene-networks.net/artiva-2/
Algorithm available in a R package that is a statistical framework to infer time-varying structures of gene-regulation networks.
Proper citation: ARTIVA (RRID:SCR_011946) Copy
http://www.phrap.org/phredphrapconsed.html
A software program for assembling shotgun DNA sequence data.
Proper citation: Phrap (RRID:SCR_011917) Copy
http://denovoassembler.sourceforge.net/
Software for a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers.
Proper citation: Ray Meta (RRID:SCR_011918) Copy
http://genome.ucsc.edu/cgi-bin/hgBlat?command=start
Software designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.
Proper citation: BLAT (RRID:SCR_011919) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2019. Delivers public cloud infrastructure that''s business grade, open source-based, and developer focused., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: HP Public Cloud (RRID:SCR_011873) Copy
High-performance cloud infrastructure and big data analytics company, offering organizations of any size the best public and hybrid cloud infrastructure for today''s demanding real-time web and mobile applications.
Proper citation: Joyent (RRID:SCR_011874) Copy
http://www.bios.unc.edu/research/genomic_software/BBSeq/
A Powerful and Flexible Approach to the Analysis of RNA Sequence Count Data.
Proper citation: BBSeq (RRID:SCR_011877) Copy
http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/
Software for an iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth.
Proper citation: IDBA-UD (RRID:SCR_011912) Copy
http://i.cs.hku.hk/~alse/hkubrg/projects/metaidba/
Software for an iterative De Bruijn Graph De Novo short read assembler specially designed for de novo metagenomic assembly. (Please note that MetaIDBA is out of maintainance now, we recommend using IDBA-UD instead which generally performs better.)
Proper citation: Meta-IDBA (RRID:SCR_011913) Copy
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