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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
SeqtrimNEXT Resource Report Resource Website 10+ mentions |
SeqtrimNEXT (RRID:SCR_011845) | SeqtrimNEXT | software resource | A customizable and distributed pre-processing software for NGS (Next Generation Sequencing) biological data.The old version for Sanger sequences, Seqtrim, has been discontinued. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
biotools:seqtrim, OMICS_01093 | https://bio.tools/seqtrim | SCR_011845 | Seqtrim | 2026-09-19 12:52:19 | 29 | |||||||
|
TagCleaner Resource Report Resource Website 50+ mentions |
TagCleaner (RRID:SCR_011846) | software application, software resource, standalone software, web application | A software tool which can automatically detect and efficiently remove tag sequences from genomic and metagenomic datasets. | tag sequence, standalone software, web application, microbiome, genomic, metagenomic, datasets |
is listed by: OMICtools is listed by: Human Microbiome Project has parent organization: SourceForge |
Available for download | OMICS_01094 | SCR_011846 | 2026-09-19 12:52:19 | 65 | |||||||||
|
Prodigal Resource Report Resource Website 1000+ mentions |
Prodigal (RRID:SCR_011936) | Prodigal | simulation software, software application, software resource | Software tool for protein coding gene prediction for prokaryotic genomes. |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: Oak Ridge National Laboratory |
PMID:20211023 | Free, Available for download, Freely available | SCR_021246, OMICS_01493 | https://sources.debian.org/src/prodigal/ | http://prodigal.ornl.gov/ | SCR_011936 | , PROkaryotic DYnamic programming Gene-finding ALgorithm, Prokaryotic Dynamic Programming Genefinding Algorithm | 2026-09-19 12:52:21 | 3398 | |||||
|
Oases Resource Report Resource Website 100+ mentions |
Oases (RRID:SCR_011896) | Oases | software resource | 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. | bio.tools, transcriptome assembler |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: European Bioinformatics Institute |
DOI:10.1093/bioinformatics/bts094 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01322, biotools:oases | https://bio.tools/oases | https://sources.debian.org/src/oases/ | SCR_011896 | 2026-09-19 12:52:20 | 289 | |||||
|
Rnnotator Resource Report Resource Website 10+ mentions |
Rnnotator (RRID:SCR_011897) | Rnnotator | software resource | Software designed to assemble Illumina single or paired-end reads. |
is listed by: OMICtools has parent organization: Brown University; Rhode Island; USA |
OMICS_01323 | SCR_011897 | 2026-09-19 12:52:20 | 24 | ||||||||||
|
GeneMark Resource Report Resource Website 500+ mentions |
GeneMark (RRID:SCR_011930) | GeneMark | analysis service resource, data analysis service, production service resource, service resource, software resource | A family of gene prediction programs developed at Georgia Institute of Technology. |
is listed by: OMICtools has parent organization: Georgia Institute of Technology; Georgia; USA |
Academic License Agreement | OMICS_01485 | SCR_011930 | 2026-09-19 12:52:21 | 805 | |||||||||
|
STM Resource Report Resource Website |
STM (RRID:SCR_011898) | STM | software resource | A de novo transcriptome assembly from next-generation sequencing data. | is listed by: OMICtools | OMICS_01325 | SCR_011898 | 2026-09-19 12:52:20 | 0 | ||||||||||
|
TopHat-Fusion Resource Report Resource Website 100+ mentions |
TopHat-Fusion (RRID:SCR_011899) | TopHat-Fusion | software resource | 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. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Maryland; Maryland; USA |
PMID:21835007 | OMICS_01359, biotools:tophat-fusion | https://bio.tools/tophat-fusion | SCR_011899 | TopHat-Fusion: An algorithm for Discovery of Novel Fusion Transcripts | 2026-09-19 12:52:20 | 162 | ||||||
|
Glimmer-MG Resource Report Resource Website 1+ mentions |
Glimmer-MG (RRID:SCR_011932) | Glimmer-MG | software resource | A software system for finding genes in environmental shotgun DNA sequences. | metagenomics, gene |
is listed by: OMICtools is related to: Glimmer has parent organization: University of Maryland; Maryland; USA |
Open unspecified license, OSI certified | OMICS_01487 | SCR_011932 | Glimmer-MG: Metagenomics Gene-Finding System, Gene Locator and Interpolated Markov ModelER - MetaGenomics | 2026-09-19 12:52:21 | 9 | |||||||
|
MetaGeneAnnotator Resource Report Resource Website 50+ mentions |
MetaGeneAnnotator (RRID:SCR_011934) | MetaGeneAnnotator | software resource | A gene-finding software program for prokaryote and phage., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01490 | SCR_011934 | 2026-09-19 12:52:21 | 88 | |||||||||
|
MGC Resource Report Resource Website |
MGC (RRID:SCR_011935) | MGC | software resource | A software application for finding complete and incomplete genes in metagenomic reads. |
is used by: EMBRYS is listed by: OMICtools |
OMICS_01491 | SCR_011935 | 2026-09-19 12:52:21 | 0 | ||||||||||
|
MetaSim Resource Report Resource Website 10+ mentions |
MetaSim (RRID:SCR_011940) | MetaSim | software resource | A Sequencing Simulator for Genomics and Metagenomics. | is listed by: OMICtools | OMICS_01509 | SCR_011940 | 2026-09-19 12:52:21 | 40 | ||||||||||
|
MEGAN Resource Report Resource Website 1000+ mentions |
MEGAN (RRID:SCR_011942) | MEGAN | software resource | Software for analyzing metagenomes. | is listed by: OMICtools | OMICS_01516 | SCR_011942 | 2026-09-19 12:52:21 | 1439 | ||||||||||
|
MOCAT Resource Report Resource Website 10+ mentions |
MOCAT (RRID:SCR_011943) | MOCAT | software resource | Software package for analyzing metagenomics datasets. |
is listed by: OMICtools has parent organization: European Molecular Biology Laboratory |
OMICS_01517 | SCR_011943 | 2026-09-19 12:52:21 | 42 | ||||||||||
|
pyGCluster Resource Report Resource Website 1+ mentions |
pyGCluster (RRID:SCR_011944) | pyGCluster | software resource | A clustering algorithm focusing on noise injection for subsequent cluster validation. | is listed by: OMICtools | PMID:24177716 | OMICS_01573 | SCR_011944 | 2026-09-19 12:52:21 | 1 | |||||||||
|
ARTIVA Resource Report Resource Website |
ARTIVA (RRID:SCR_011946) | ARTIVA | software resource | Algorithm available in a R package that is a statistical framework to infer time-varying structures of gene-regulation networks. | r | is listed by: OMICtools | PMID:20860793 | Free, Public | OMICS_01680 | SCR_011946 | Auto Regressive TIme VArying regulatory models | 2026-09-19 12:52:21 | 0 | ||||||
|
APHL Resource Report Resource Website 10+ mentions |
APHL (RRID:SCR_012001) | APHL | nonprofit organization | Works to strengthen laboratories serving the public''s health in the US and globally. | is listed by: OMICtools | Wikidata: Q4810010, Crossref funder ID: 100008482, ISNI: 0000 0001 0029 6188, OMICS_01790, grid.422961.a | https://ror.org/04d0f7957 | SCR_012001 | Association of Public Health Laboratories | 2026-09-19 12:52:22 | 10 | ||||||||
|
MetAMOS Resource Report Resource Website 10+ mentions |
MetAMOS (RRID:SCR_011914) | MetAMOS | data processing software, software application, software resource, workflow software | A modular and open source metagenomic assembly and analysis pipeline. | microbiome, pipeline, microbiome, workflow software, metagenomic assembly, metagenomic assembly, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: bio.tools is listed by: Debian is hosted by: GitHub |
Open source, Available for download | OMICS_01426, biotools:metamos | https://github.com/marbl/metAMOS, https://bio.tools/metamos | SCR_011914 | 2026-09-19 12:52:21 | 14 | |||||||
|
Phrap Resource Report Resource Website 100+ mentions |
Phrap (RRID:SCR_011917) | Phrap | software resource | A software program for assembling shotgun DNA sequence data. | is listed by: OMICtools | Free to academic users | OMICS_01429 | SCR_011917 | 2026-09-19 12:52:21 | 376 | |||||||||
|
Ray Meta Resource Report Resource Website 10+ mentions |
Ray Meta (RRID:SCR_011918) | Ray Meta | software resource | Software for a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23259615 | Free | OMICS_01431 | SCR_011918 | 2026-09-19 12:52:21 | 12 |
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