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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
University of Tennessee; Tennessee; USA Resource Report Resource Website 1+ mentions |
University of Tennessee; Tennessee; USA (RRID:SCR_011712) | UT | university | University of Tennessee System is comprised of campuses at Knoxville, Chattanooga, Pulaski and Martin; Health Science Center at Memphis; Space Institute at Tullahoma; and statewide Institute of Agriculture and Institute for Public Service. |
is parent organization of: University of Tennessee Health Science Center; Tennessee; USA is parent organization of: University of Tennessee Knoxville; Tennessee; USA is parent organization of: University of Tennessee KnoxvilleAdvanced Microscopy and Imaging Center AMIC Core Facility is parent organization of: University of Tennessee at Knoxville Genomics Core Facility |
, Crossref Funder ID 100014455, GRID grid.411461.7, nlx_14003, ISNI 0000 0001 2315 1184, Wikidata Q1150105 | https://ror.org/020f3ap87 | SCR_011712 | University of Tennessee | 2026-09-12 12:57:38 | 2 | ||||||||
|
MT-Toolbox Resource Report Resource Website 1+ mentions |
MT-Toolbox (RRID:SCR_011833) | MT-Toolbox | software resource | A software package for building accurate ConSeqs from tagged reads. | is listed by: OMICtools | PMID:23995388 | BSD License | OMICS_01058 | SCR_011833 | Molecule Tag Toolbox | 2026-09-12 12:57:40 | 4 | |||||||
|
AlienTrimmer Resource Report Resource Website 50+ mentions |
AlienTrimmer (RRID:SCR_011835) | AlienTrimmer | software resource | Allows detecting and removing multiple alien sequences in both ends of sequence reads. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23912058 | Free | biotools:alientrimmer, OMICS_01082 | https://bio.tools/alientrimmer | SCR_011835 | 2026-09-12 12:57:40 | 74 | ||||||
|
University of the Sciences in Philadelphia College of Pharmacy Resource Report Resource Website |
University of the Sciences in Philadelphia College of Pharmacy (RRID:SCR_011728) | data or information resource, degree granting program, graduate program resource, institution, organization portal, portal, training resource, undergraduate program resource, university | Pharmaceutical education began at Philadelphia College of Pharmacy (PCP), the first such institution in North America. With nearly two centuries of experience in pharmacy and science and thousands of alumni working in the healthcare industry, the world turns to PCP graduates for advice. From undergraduate majors to graduate degrees to our esteemed PharmD program, you can learn where the founders (alumni such as McNeil, Lilly, Rorer, Wyeth, Warner, Burroughs, and Wellcome) of six of the top pharmaceutical companies in the world got their education. Since 1821, they have been preparing professionals in pharmacy practice, science, and health care. There is no better place than PCP to prepare you for a lifelong career in the healthcare industry. | has parent organization: University of Sciences in Philadelphia; Pennsylvania; USA | nlx_16974 | SCR_011728 | PCP College of Pharmacy | 2026-09-12 12:57:39 | 0 | ||||||||||
|
University of Texas at Tyler; Texas; USA Resource Report Resource Website 1+ mentions |
University of Texas at Tyler; Texas; USA (RRID:SCR_011720) | university | Public university in Tyler, Texas. Founded in 1971, it is a part of the University of Texas System. |
is parent organization of: SRPDB is parent organization of: tmRNA Database |
Wikidata:Q212528, ISNI:0000 0001 0626 4654, nlx_48968, grid.267327.5 | https://ror.org/01azfw069 | SCR_011720 | UTT | 2026-09-12 12:57:38 | 1 | |||||||||
|
QTrim Resource Report Resource Website 1+ mentions |
QTrim (RRID:SCR_011842) | QTrim | software resource | A next generation sequence quality trimming tool. | is listed by: OMICtools | OMICS_01089 | SCR_011842 | 2026-09-12 12:57:40 | 6 | ||||||||||
|
sabre Resource Report Resource Website 100+ mentions |
sabre (RRID:SCR_011843) | sabre | data analysis software, data processing software, software application, software resource | Software tool to demultiplex barcoded reads into separate files. Works on both single-end and paired-end data in fastq format. Used in next generation sequencing to analyze a broad range of data. | demultiplex, bardcode, separate, fastq, format, data, next, generation, sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:sabre, OMICS_01090 | https://bio.tools/sabre | SCR_011843 | Systems Approach to Biomarker Research | 2026-09-12 12:57:40 | 219 | ||||||
|
Scythe Resource Report Resource Website 100+ mentions |
Scythe (RRID:SCR_011844) | Scythe | software resource | Scythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. |
is listed by: OMICtools is listed by: Debian |
OMICS_01091 | https://sources.debian.org/src/scythe/ | SCR_011844 | Scythe - A Bayesian adapter trimmer | 2026-09-12 12:57:40 | 189 | ||||||||
|
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 | 2026-09-12 12:57:40 | 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 | 2026-09-12 12:57:41 | 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 | 2026-09-12 12:57:42 | 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 | 2026-09-12 12:57:41 | 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 | 2026-09-12 12:57:41 | 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 | 2026-09-12 12:57:42 | 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 | 2026-09-12 12:57:41 | 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 | 2026-09-12 12:57:41 | 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 | 2026-09-12 12:57:42 | 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 | 2026-09-12 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 |
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The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
