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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 | 2026-09-03 04:51:20 | 29 | |||||||
|
University of Texas System; Texas; USA Resource Report Resource Website |
University of Texas System; Texas; USA (RRID:SCR_011725) | UT System | university | 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. |
is parent organization of: University of Texas Medical Branch at Galveston is parent organization of: University of Texas MD Anderson Cancer Center is parent organization of: University of Texas at El Paso is parent organization of: University of Texas Health Science Center at Houston; Texas; USA is parent organization of: University of Texas Southwestern Medical Center; Texas; USA |
Wikidata:Q2140391, nlx_61301, Crossref funder ID:100007130, ISNI:121548364, grid.55460.32 | https://ror.org/01gek1696 | SCR_011725 | University of Texas System | 2026-09-03 04:51:16 | 0 | ||||||||
|
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 | 2026-09-03 04:51:34 | 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 | 2026-09-03 04:51:59 | 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 | 2026-09-03 04:51:21 | 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 | 2026-09-03 04:51:22 | 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 | 2026-09-03 04:51:39 | 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 | 2026-09-03 04:51:33 | 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 | 2026-09-03 04:51:25 | 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 | 2026-09-03 04:51:34 | 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 | 2026-09-03 04:52:01 | 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 | 2026-09-03 04:51:35 | 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 | 2026-09-03 04:51:34 | 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 | 2026-09-03 04:51:23 | 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 | 2026-09-03 04:51:41 | 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 | 2026-09-03 04:51:25 | 0 | ||||||
|
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 | 2026-09-03 04:51:34 | 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 | 2026-09-03 04:52:00 | 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 | 2026-09-03 04:51:33 | 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 | 2026-09-03 04:51:22 | 3808 |
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