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http://www.scbi.uma.es/ingebiol/session/new/seqtrimnext

A customizable and distributed pre-processing software for NGS (Next Generation Sequencing) biological data.The old version for Sanger sequences, Seqtrim, has been discontinued.

Proper citation: SeqtrimNEXT (RRID:SCR_011845) Copy   

•   Source: SciCrunch Registry

http://www.utsystem.edu/

The mission of The University of Texas System is to provide high-quality educational opportunities for the enhancement of the human resources of Texas, the nation, and the world through intellectual and personal growth. Established by the Texas Constitution in 1876, The University of Texas System consists of nine academic universities and six health institutions. The System administration is based in Austin, Texas. Offices are also located in Midland, Texas (University Lands/West Texas Operations) and Washington, D.C. (Federal Relations). These offices are responsible for the central management and coordination of the academic and health institutions. The System has a special responsibility for managing the Permanent University Fund (PUF), other endowments, managing university lands, carrying out the Board of Regents'' policies, collaborating with the Board of Regents on strategic planning, and serving as consultants to the institutions on issues ranging from academic programs to fund raising. In addition, the System provides a wide range of centralized, cost-effective, and value-added services on behalf of the UT institutions and the public.

Proper citation: University of Texas System; Texas; USA (RRID:SCR_011725) Copy   

•   Source: SciCrunch Registry

https://github.com/hyattpd/Prodigal

Software tool for protein coding gene prediction for prokaryotic genomes.

Proper citation: Prodigal (RRID:SCR_011936) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://opal.biology.gatech.edu/GeneMark/

A family of gene prediction programs developed at Georgia Institute of Technology.

Proper citation: GeneMark (RRID:SCR_011930) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://ab.inf.uni-tuebingen.de/software/metasim/

A Sequencing Simulator for Genomics and Metagenomics.

Proper citation: MetaSim (RRID:SCR_011940) Copy   

•   Source: SciCrunch Registry

http://ab.inf.uni-tuebingen.de/software/megan/

Software for analyzing metagenomes.

Proper citation: MEGAN (RRID:SCR_011942) Copy   

•   Source: SciCrunch Registry

http://vm-lux.embl.de/~kultima/MOCAT//

Software package for analyzing metagenomics datasets.

Proper citation: MOCAT (RRID:SCR_011943) Copy   

•   Source: SciCrunch Registry

http://pygcluster.github.io/

A clustering algorithm focusing on noise injection for subsequent cluster validation.

Proper citation: pyGCluster (RRID:SCR_011944) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://cbcb.umd.edu/software/metAMOS

A modular and open source metagenomic assembly and analysis pipeline.

Proper citation: MetAMOS (RRID:SCR_011914) Copy   

•   Source: SciCrunch Registry

http://www.phrap.org/phredphrapconsed.html

A software program for assembling shotgun DNA sequence data.

Proper citation: Phrap (RRID:SCR_011917) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry