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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-09-12 12:57:42 | 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 | 2026-09-12 12:57:42 | 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 | 2026-09-12 12:57:42 | 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 | 2026-09-12 12:57:42 | 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 | 2026-09-12 12:57:42 | 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 | 2026-09-12 12:57:42 | 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 | 2026-09-12 12:57:42 | 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 | 2026-09-12 12:57:43 | 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 | 2026-09-12 12:57:42 | 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 | 2026-09-12 12:57:42 | 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 | 2026-09-12 12:57:42 | 12 | |||||||
|
BLAT Resource Report Resource Website 1000+ mentions |
BLAT (RRID:SCR_011919) | BLAT | software resource | Software designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. | bio.tools |
is used by: deFuse is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Santa Cruz; California; USA is required by: RelocaTE |
biotools:blat, OMICS_01434 | https://bio.tools/blat | SCR_011919 | 2026-09-12 12:57:42 | 3808 | ||||||||
|
HP Public Cloud Resource Report Resource Website 1+ mentions |
HP Public Cloud (RRID:SCR_011873) | HP Public Cloud | service resource | 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. | cloud, computing, storage, platform | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01205 | SCR_011873 | 2026-09-12 12:57:41 | 2 | ||||||||
|
1DegreeBio Resource Report Resource Website 10+ mentions |
1DegreeBio (RRID:SCR_011994) | software resource | A registry which provides links and reviews for material resources such as reagents, equipment, digital tools, and providers, as well as the companies that sell them. Users can search for specific materials or search by vendor, product, or service type. | registry, reagents, equipment, digital tool, marketplace, service provider, review |
is listed by: OMICtools is listed by: Connected Researchers is related to: Connected Researchers |
Free, Public | OMICS_01765 | SCR_011994 | 1degreebio, 1degreebio.org | 2026-09-12 12:57:43 | 13 | ||||||||
|
Joyent Resource Report Resource Website |
Joyent (RRID:SCR_011874) | Joyent | service resource | 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. | cloud, big data | is listed by: OMICtools | For a fee | OMICS_01206 | SCR_011874 | 2026-09-12 12:57:41 | 0 | ||||||||
|
Antibody Portal Resource Report Resource Website |
Antibody Portal (RRID:SCR_011995) | Antibody Portal | antibody supplier, commercial organization, material resource, reagent supplier | Serves as a gateway that provides visible access to a large number of reagents and accompanying characterization data to the research and industrial community. | is listed by: OMICtools | OMICS_01767 | SCR_011995 | 2026-09-12 12:57:43 | 0 | ||||||||||
|
Antibody Validation Database Resource Report Resource Website 10+ mentions |
Antibody Validation Database (RRID:SCR_011996) | Antibody Validation Database | data or information resource, data repository, database, service resource, storage service resource | The aim of this site is to collect and to share experimental results on antibodies that would otherwise remain in laboratories, thus aiding researchers in selection and validation of antibodies. | is listed by: OMICtools | NHGRI U01 HG004258; NHGRI U01 HG004270; OER U01 ES017166 |
The community can contribute to this resource | OMICS_01769 | SCR_011996 | 2026-09-12 12:57:43 | 15 | ||||||||
|
BBSeq Resource Report Resource Website 1+ mentions |
BBSeq (RRID:SCR_011877) | BBSeq | software resource | A Powerful and Flexible Approach to the Analysis of RNA Sequence Count Data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
biotools:bbseq, OMICS_01300 | https://bio.tools/bbseq | SCR_011877 | 2026-09-12 12:57:41 | 3 | ||||||||
|
IDBA-UD Resource Report Resource Website 500+ mentions |
IDBA-UD (RRID:SCR_011912) | IDBA-UD | software resource | Software for an iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. |
is listed by: OMICtools is listed by: Debian is related to: Meta-IDBA |
PMID:22495754 DOI:10.1093/bioinformatics/bts174 |
Acknowledgement requested | OMICS_01423 | https://sources.debian.org/src/idba/ | SCR_011912 | 2026-09-12 12:57:42 | 524 | |||||||
|
Meta-IDBA Resource Report Resource Website 1+ mentions |
Meta-IDBA (RRID:SCR_011913) | Meta-IDBA | software resource | 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.) |
is listed by: OMICtools is related to: IDBA-UD |
PMID:21685107 | Acknowledgement requested | OMICS_01425 | SCR_011913 | 2026-09-12 12:57:42 | 9 |
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