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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Mutation Surveyor Resource Report Resource Website 500+ mentions |
Mutation Surveyor (RRID:SCR_001247) | data processing software, software application, sequence analysis software, data analysis software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for DNA sequencing analysis that integates with Sanger Sequencing files generated by Applied Biosystems Genetic Analyzers, MegaBACE, and Beckman CEQ electrophoresis systems. It can be used to find single nucleotide polymorphisms (SNPs), insertions and deletions (INDELS), and somatic mutations in direct sequencing, PCR sequencing, mitochondrial DNA sequencing, and resequencing projects. | dna, sequencing, dna-seq, sanger sequencing, sequence analysis software | is listed by: OMICtools | PMID:21780000 PMID:20938837 |
Restricted | OMICS_01816 | Mutation Surveyor software version 5.0 | http://www.softgenetics.com/mutationSurveyor.html | SCR_001247 | 2026-08-05 10:43:19 | 668 | ||||||
|
AutoAssemblyD Resource Report Resource Website |
AutoAssemblyD (RRID:SCR_001087) | data processing software, software application, sequence analysis software, data analysis software, software resource | Software which performs local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers. | genome, genome assembly, xml, sequence analysis software, local genome assembly, remote genome assembly, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24143057 | Free, Available for download, Freely available | biotools:autoassemblyd, OMICS_00874 | https://bio.tools/autoassemblyd | SCR_001087 | 2026-08-05 10:43:18 | 0 | |||||||
|
GenoSet Resource Report Resource Website |
GenoSet (RRID:SCR_001275) | GenoSet | software resource, data processing software, software application, data analysis software | Software package to load, manipulate, and plot copynumber and BAF data by providing classes similar to ExpressionSet for copy number analysis. The class extends ExpressionSet by adding a locData slot for a RangedData or GRanegs object. This object contains feature genome location data and provides for efficient subsetting on genome location. CNSet and BAFSet extend GenoSet and require assayData matrices for Copy Number (cn) or Log-R Ratio (lrr) and B-Allele Frequency (baf) data. Implements and provides convenience functions for processing of copy number and B-Allele Frequency data. | copy number variation, data representation, infrastructure, microarray, snp |
is listed by: OMICtools has parent organization: Bioconductor |
Artistic License, v2 | OMICS_02063 | SCR_001275 | genoset - Provides classes similar to ExpressionSet for copy number analysis | 2026-08-05 10:43:20 | 0 | |||||||
|
Prodigal Resource Report Resource Website 1000+ mentions |
Prodigal (RRID:SCR_011936) | Prodigal | software application, simulation software, 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 | 2026-08-05 10:45:38 | 2985 | |||||
|
GeneMark Resource Report Resource Website 500+ mentions |
GeneMark (RRID:SCR_011930) | GeneMark | software resource, data analysis service, production service resource, service resource, analysis service 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 | 2026-08-05 10:45:37 | 768 | |||||||||
|
Annmap Resource Report Resource Website 1+ mentions |
Annmap (RRID:SCR_011783) | Annmap | software resource, data or information resource, database | A genome browser that includes mappings between genomic features and Affymetrix microarrays. Associated with annmap is: * a Bioconductor package, annmap that provides programmatic access to the underlying MySQL database tables (which are freely available for download on this site) * xmapbridge, a Bioconductor package that outputs numeric data in a form suitable for presentation in the browser. This is supported by XMapBridge, a Java client that sits on the local desktop and performs the graph rendering for the browser. | is listed by: OMICtools | Cancer Research UK ; Cancer Research UK Manchester Institute |
OMICS_00900 | SCR_011783 | 2026-08-05 10:45:36 | 6 | |||||||||
|
B-Fabric Resource Report Resource Website 1+ mentions |
B-Fabric (RRID:SCR_011827) | B-Fabric | data or information resource, data repository, database, storage service resource, service resource | An open infrastructure for managing projects and data in life sciences that allows to store and access experimental data together with its scientific context. The platform connects the data from scientific instruments with data analysis tools, including workflow, annotation, and data visualization support. All public data can be searched and used to carry out inter-experiment analyses. For a fee, B-Fabric Order allows you to order the following analytical services at the FGCZ independent of a User Lab research project: Mass spectrometry, Protein sequencing, peptide sequencing, Amino acid analysis, Chromatography, Electrophoresis. | project management, mass spectrometry, protein sequencing, peptide sequencing, amino acid analysis, chromatography, electrophoresis |
is listed by: OMICtools has parent organization: University of Zurich; Zurich; Switzerland |
PMID:21772064 | Account required | OMICS_01002 | SCR_011827 | 2026-08-05 10:45:37 | 1 | |||||||
|
TBLASTX Resource Report Resource Website 1000+ mentions |
TBLASTX (RRID:SCR_011823) | TBLASTX | software resource, web application | A web-based tool used to search translated nucleotide databases using a translated nucleotide query. | nucleotide database, web based, nucleotide query |
is listed by: OMICtools has parent organization: NCBI |
Available to the research community | OMICS_01000 | SCR_011823 | Translated BLAST: tblastx | 2026-08-05 10:45:37 | 1446 | |||||||
|
MetAMOS Resource Report Resource Website 10+ mentions |
MetAMOS (RRID:SCR_011914) | MetAMOS | data processing software, software application, workflow software, software resource | 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 | 2026-08-05 10:45:37 | 14 | |||||||
|
Antibody Portal Resource Report Resource Website |
Antibody Portal (RRID:SCR_011995) | Antibody Portal | material resource, commercial organization, reagent supplier, antibody 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 | 2026-08-05 10:45:38 | 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, storage service resource, 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 | OER U01 ES017166; NHGRI U01 HG004258; NHGRI U01 HG004270 |
The community can contribute to this resource | OMICS_01769 | SCR_011996 | 2026-08-05 10:45:38 | 14 | ||||||||
|
KisSplice Resource Report Resource Website 10+ mentions |
KisSplice (RRID:SCR_011893) | KisSplice | software resource, data processing software, software application, data analysis software | Software tool that enables analysis of RNA-seq data with or without reference genome. Local transcriptome assembler for SNPs, indels and AS events. | RNA-seq data analysis, with reference genome, without reference genome, local transcriptome assembler, SNPs, indels, AS events., bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1186/1471-2105-13-S6-S5 | Free, Available for download, Freely available | biotools:KisSplice, OMICS_01321 | https://bio.tools/KisSplice, https://sources.debian.org/src/kissplice/ | SCR_011893 | 2026-08-05 10:45:37 | 20 | ||||||
|
ECHO Resource Report Resource Website 100+ mentions |
ECHO (RRID:SCR_011851) | ECHO | data processing software, algorithm resource, software application, data analysis software, sequence analysis software, software resource | Error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina''s Genome Analyzer II. | error correction, rnaseq, rna sequence, short-read, next-generation sequencing, ngs, illumina, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21482625 DOI:10.1101/gr.111351.110 |
Free, Available for download | biotools:echo, OMICS_01102 | https://bio.tools/echo, https://sources.debian.org/src/uc-echo/ | SCR_011851 | ECHO: A reference-free short-read error correction algorithm | 2026-08-05 10:45:37 | 310 | |||||
|
CaMPDB Resource Report Resource Website 1+ mentions |
CaMPDB (RRID:SCR_011976) | CaMPDB | data or information resource, database, data analysis service, production service resource, service resource, analysis service resource | Calpain cleavage prediction using multiple kernel learning. | is listed by: OMICtools | PMID:21559271 | OMICS_01669 | SCR_011976 | Calpain for Modulatory Proteolysis Database | 2026-08-05 10:45:38 | 7 | ||||||||
|
Algal Functional Annotation Tool Resource Report Resource Website |
Algal Functional Annotation Tool (RRID:SCR_012034) | Algal Functional Annotation Tool | data or information resource, database, data analysis service, production service resource, service resource, analysis service resource | Tools to search gene lists for functional term enrichment as well as to dynamically visualize proteins onto pathway maps. Additionally, integrated expression data may be used to discover similarly expressed genes based on a starting gene of interest. | gene, pathway, visualization, annotation, function, protein family, ontology, protein, genomics |
is listed by: OMICtools is related to: Gene Ontology is related to: KEGG is related to: MetaCyc is related to: Reactome is related to: Pfam is related to: InterPro has parent organization: University of California at Los Angeles; California; USA |
DOE ; NAABB ; IGP ; Air Force Office of Scientific Research |
PMID:21749710 | OMICS_02226 | SCR_012034 | 2026-08-05 10:45:39 | 0 | |||||||
|
NGS Leaders Resource Report Resource Website |
NGS Leaders (RRID:SCR_011982) | NGS Leaders | community building portal, data or information resource, portal | A community created to advance the use and value of next-generation sequencing through knowledge sharing. | is listed by: OMICtools | OMICS_01707 | SCR_011982 | 2026-08-05 10:45:38 | 0 | ||||||||||
|
Stack Overflow Resource Report Resource Website 10+ mentions |
Stack Overflow (RRID:SCR_011984) | Stack Overflow | community building portal, data or information resource, portal | A question and answer site for professional and enthusiast programmers. | programmer | is listed by: OMICtools | Free | OMICS_01711 | SCR_011984 | 2026-08-05 10:45:38 | 20 | ||||||||
|
Bioinformaticsweb Resource Report Resource Website |
Bioinformaticsweb (RRID:SCR_011988) | BIW | data or information resource, topical portal, portal | Open Access Bioinformatics resource portal. | bioinformatics | is listed by: OMICtools | Free | OMICS_01729 | SCR_011988 | 2026-08-05 10:45:38 | 0 | ||||||||
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HTS Mappers Resource Report Resource Website 1+ mentions |
HTS Mappers (RRID:SCR_011991) | HTS Mappers | data or information resource, software repository, software resource, data set | Data set providing an up-to-date compendium of HTS mappers initially provided in the article Tools for mapping high-throughput sequencing data. Please let fill out the provided form if you are a developer and your mapper is not listed or you want to update the data for your mapper. | mapping, high-throughput sequencing, dna, rna, mirna, bisulfite, mapper |
is listed by: OMICtools has parent organization: European Bioinformatics Institute |
PMID:23060614 | OMICS_01733 | SCR_011991 | 2026-08-05 10:45:38 | 2 | ||||||||
|
Next Generation Sequencing WikiBook Resource Report Resource Website |
Next Generation Sequencing WikiBook (RRID:SCR_011993) | NGS WikiBook | book, data or information resource, wiki, narrative resource | The Need for an Up-To-Date Synthesis of Next Generation Sequencing Know-How. |
is listed by: OMICtools has parent organization: Wikibooks |
OMICS_01744 | SCR_011993 | The NGS WikiBook | 2026-08-05 10:45:38 | 0 |
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