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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Crossbow Resource Report Resource Website 1+ mentions |
Crossbow (RRID:SCR_013306) | Crossbow | software resource | A scalable software pipeline for whole genome resequencing analysis. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19930550 DOI:10.1186/gb-2009-10-11-r134 |
biotools:crossbow, OMICS_00284 | https://bio.tools/crossbow | https://sources.debian.org/src/crossbow/ | SCR_013306 | 2026-08-08 12:00:21 | 5 | ||||||
|
INCLUSive Resource Report Resource Website 1+ mentions |
INCLUSive (RRID:SCR_013488) | INCLUSive | software resource | A suit of algorithms and tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:12824346 | Acknowledgement requested | OMICS_00766, biotools:inclusive | https://bio.tools/inclusive | SCR_013488 | 2026-08-08 11:59:56 | 7 | ||||||
|
MED Resource Report Resource Website 1+ mentions |
MED (RRID:SCR_013403) | MED | software resource | A non-supervised gene prediction algorithm for prokaryotic genomes with multivariate entropy distance method. | prokaryotic, genome, multivariate entropy distance | is listed by: OMICtools | PMID:17367537 | OMICS_01489 | SCR_013403 | 2026-08-08 12:00:21 | 1 | ||||||||
|
Alta-Cyclic Resource Report Resource Website |
Alta-Cyclic (RRID:SCR_013373) | Alta-Cyclic | software resource | An Illumina Genome-Analyzer (Solexa) base caller. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Cold Spring Harbor Laboratory |
OMICS_01149, biotools:alta-cyclic | https://bio.tools/alta-cyclic | SCR_013373 | 2026-08-08 12:00:21 | 0 | ||||||||
|
Explicet Resource Report Resource Website 50+ mentions |
Explicet (RRID:SCR_011937) | Explicet | software resource | Graphical user interface software for metadata-driven management, analysis, and visualization of microbiome data. | is listed by: OMICtools | OMICS_01497 | SCR_011937 | 2026-08-08 11:59:37 | 60 | ||||||||||
|
MetaSee Resource Report Resource Website 1+ mentions |
MetaSee (RRID:SCR_011938) | MetaSee | software resource | An online toolbox for metagenomic data visualization. | is listed by: OMICtools | OMICS_01499 | SCR_011938 | 2026-08-08 11:59:55 | 3 | ||||||||||
|
SynTView Resource Report Resource Website 1+ mentions |
SynTView (RRID:SCR_011939) | SynTView | software resource | An interactive multi-view genome browser for next-generation comparative microorganism genomics. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01500, biotools:syntview | https://bio.tools/syntview | SCR_011939 | 2026-08-08 12:00:03 | 7 | ||||||||
|
Glimmer Resource Report Resource Website 500+ mentions |
Glimmer (RRID:SCR_011931) | Glimmer | production service resource, software resource, data analysis service, analysis service resource, service resource | A software system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. | microbial, gene, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Glimmer-MG is related to: GlimmerHMM has parent organization: Johns Hopkins University; Maryland; USA |
DOI:10.1093/nar/26.2.544 | Open unspecified license, OSI certified | OMICS_01486, biotools:glimmer | https://bio.tools/glimmer, https://sources.debian.org/src/tigr-glimmer/ | SCR_011931 | Glimmer - Microbial Gene-Finding System | 2026-08-08 11:59:55 | 687 | |||||
|
NeSSM Resource Report Resource Website 10+ mentions |
NeSSM (RRID:SCR_011941) | NeSSM | software resource | A Next-Generation Sequencing Simulator for Metagenomics. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01510, biotools:nessm | https://bio.tools/nessm | SCR_011941 | 2026-08-08 11:59:55 | 11 | ||||||||
|
MetaVelvet Resource Report Resource Website 50+ mentions |
MetaVelvet (RRID:SCR_011915) | MetaVelvet | software resource | Software for a short read de novo metagenome assembly created by modifying and extending a single-genome and de Bruijn-graph based assembler, Velvet. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01427, biotools:metavelvet | https://bio.tools/metavelvet | SCR_011915 | MetaVelvet: a short read assember for metagenomics | 2026-08-08 12:00:02 | 78 | |||||||
|
Newbler Resource Report Resource Website 1000+ mentions |
Newbler (RRID:SCR_011916) | Newbler | software resource | A software package for de novo DNA sequence assembly. |
is listed by: OMICtools has parent organization: University of Arizona; Arizona; USA |
OMICS_01428 | SCR_011916 | 2026-08-08 11:59:37 | 1343 | ||||||||||
|
Rackspace Resource Report Resource Website 1+ mentions |
Rackspace (RRID:SCR_011875) | Rackspace | service resource | An open cloud company with performance Cloud Servers that offer 100% SSD storage & 10Gb Ethernet networking for your demanding applications. | cloud | is listed by: OMICtools | For a fee | OMICS_01207 | SCR_011875 | 2026-08-08 11:59:36 | 3 | ||||||||
|
VirtualBox Resource Report Resource Website 50+ mentions |
VirtualBox (RRID:SCR_011876) | VirtualBox | software resource | A general-purpose full virtualizer for x86 and AMD64/Intel64 hardware, targeted at server, desktop and embedded use. | is listed by: OMICtools | GNU General Public License, v2 | OMICS_01208 | SCR_011876 | 2026-08-08 11:59:54 | 99 | |||||||||
|
GeneStitch Resource Report Resource Website |
GeneStitch (RRID:SCR_011910) | GeneStitch | software resource | Network Matching Algorithm using the de Bruijn graph assembly of metagenomes to improve the assembly of genes. | gene fragment, network matching, gene assembly, metagenomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Indiana University; Indiana; USA |
PMID:22962453 | Open unspecified license | OMICS_01421, biotools:genestitch | https://bio.tools/genestitch | SCR_011910 | GeneStitch: Network Matching Algorithm to Gene Assembly | 2026-08-08 11:59:37 | 0 | |||||
|
VMware Resource Report Resource Website 10+ mentions |
VMware (RRID:SCR_011878) | VMware | software resource | Software that virtualizes computing, from the data center to the cloud to mobile devices, to help customers be more agile, responsive, and profitable. | cloud, computing | is listed by: OMICtools | OMICS_01209 | SCR_011878 | 2026-08-08 11:59:36 | 23 | |||||||||
|
Genovo Resource Report Resource Website 100+ mentions |
Genovo (RRID:SCR_011911) | Genovo | software resource | Software for a novel de novo sequence assembler that discovers likely sequence reconstructions under the model. |
is listed by: OMICtools has parent organization: Stanford University; Stanford; California |
OMICS_01422 | SCR_011911 | Genovo - Metagenomic de novo Sequencing | 2026-08-08 11:59:55 | 227 | |||||||||
|
METAREP Resource Report Resource Website 1+ mentions |
METAREP (RRID:SCR_011926) | METAREP | software resource, software application, data analysis software, data processing software | A tool for high-performance comparative metagenomics that allows users to view, query, browse, and compare metagenomics annotation profiles from short reads or assemblies. Users can use statistical tests, hierarchical clustering, multidimensional scaling, and heat maps to compare multiple datasets at various functional and taxonomic levels. | microbiome, comparison, comparative metagenomics, annotation, short read, short assembly, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools has parent organization: J. Craig Venter Institute |
DOI:10.1093/bioinformatics/btq455 | Open source | biotools:metarep, OMICS_01480 | https://bio.tools/metarep | SCR_011926 | 2026-08-08 11:59:55 | 8 | ||||||
|
DNAnexus Resource Report Resource Website 100+ mentions |
DNAnexus (RRID:SCR_011884) | DNAnexus | service resource | A cloud-based platform to support genomics at your organization. | genomics, cloud computing, genomic analysis | is listed by: OMICtools | OMICS_01217 | SCR_011884 | 2026-08-08 12:00:01 | 136 | |||||||||
|
Genestack Resource Report Resource Website 1+ mentions |
Genestack (RRID:SCR_011885) | Genestack | service resource | A universal collaborative platform for bioinformatics application development that allows users to store and share large data sets securely within and across organizations, with free access to public data from major databases. The platform includes open-source and proprietary genomics applications, working together independent of file formats. For developers an SDK, APIs and a marketplace are provided. | data sharing, data management, sequencing, quality control, exome, genome, variant call, somatic mutation, rna-seq, chip-seq, data analysis, visualization, computing, big data, next-generation sequencing | is listed by: OMICtools | OMICS_01218 | SCR_011885 | 2026-08-08 11:59:36 | 2 | |||||||||
|
Globus Genomics Resource Report Resource Website 10+ mentions |
Globus Genomics (RRID:SCR_011887) | Globus Genomics | storage service resource, data repository, service resource | Software-as-a-service for big data management offering fast, reliable, secure file transfer and sharing services to non-profit researchers. It combines state-of-the-art algorithms, data management tools, a graphical workflow environment, and an elastic computing infrastructure making it easy to manipulate, store, and share your data, no matter how big it gets. | data sharing, data management, genomics |
is listed by: OMICtools has parent organization: Argonne National Laboratory |
OMICS_01220 | SCR_011887 | 2026-08-08 12:00:01 | 26 |
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