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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
cutadapt Resource Report Resource Website 5000+ mentions |
cutadapt (RRID:SCR_011841) | cutadapt | software resource | Software tool that removes adapter sequences from DNA sequencing reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is required by: SL-quant works with: Trim Galore |
DOI:10.14806/ej.17.1.200 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01086, biotools:cutadapt | https://bio.tools/cutadapt | https://sources.debian.org/src/cutadapt/ | SCR_011841 | 2026-08-01 12:04:21 | 7023 | |||||
|
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 | 2026-08-01 12:04:33 | 55 | ||||||||||
|
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 | 2026-08-01 12:04:25 | 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 | 2026-08-01 12:04:31 | 7 | ||||||||
|
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 | 2026-08-01 12:04:25 | 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 | 2026-08-01 12:04:31 | 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 | 2026-08-01 12:04:24 | 1336 | ||||||||||
|
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 | 2026-08-01 12:04:22 | 2 | ||||||||
|
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 | 2026-08-01 12:04:32 | 91 | |||||||||
|
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 | 2026-08-01 12:04:33 | 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 | 2026-08-01 12:04:31 | 21 | |||||||||
|
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 | 2026-08-01 12:04:31 | 227 | |||||||||
|
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 | 2026-08-01 12:04:22 | 125 | |||||||||
|
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 | 2026-08-01 12:04:23 | 2 | |||||||||
|
Mega BLAST Resource Report Resource Website 100+ mentions |
Mega BLAST (RRID:SCR_011920) | Mega BLAST | software resource | Software that uses the greedy algorithm for nucleotide sequence alignment search. |
is listed by: OMICtools has parent organization: NCBI |
OMICS_01435 | SCR_011920 | 2026-08-01 12:04:25 | 280 | ||||||||||
|
UCLUST algorithm Resource Report Resource Website 50+ mentions |
UCLUST algorithm (RRID:SCR_011921) | UCLUST | software resource | Algorithm that divides a set of sequences into clusters | is listed by: OMICtools | PMID:20709691 | OMICS_01448 | SCR_011921 | 2026-08-01 12:04:31 | 50 | |||||||||
|
eXPatGen Resource Report Resource Website |
eXPatGen (RRID:SCR_011922) | eXPatGen | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A simulator of gene expression patterns in order to evaluate different analysis methods, such as clustering and principle component analysis (PCA). | is listed by: OMICtools | PMID:12801875 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01572 | SCR_011922 | eXPatGen - An On-line Gene Expression Pattern Generator | 2026-08-01 12:04:33 | 0 | |||||||
|
EBARDenovo Resource Report Resource Website 1+ mentions |
EBARDenovo (RRID:SCR_011890) | EBARDenovo | software resource | Highly accurate de novo assembly of RNA-Seq with efficient chimera-detection. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01317 | SCR_011890 | 2026-08-01 12:04:23 | 2 | ||||||||||
|
IDBA-Tran Resource Report Resource Website 10+ mentions |
IDBA-Tran (RRID:SCR_011891) | IDBA-Tran | software resource | An iterative De Bruijn Graph De Novo short read assembler for transcriptome. | is listed by: OMICtools | OMICS_01318 | SCR_011891 | 2026-08-01 12:04:33 | 25 | ||||||||||
|
RACER Resource Report Resource Website 10+ mentions |
RACER (RRID:SCR_011852) | RACER | software resource | A software program for correcting errors in sequencing data. | is listed by: OMICtools | OMICS_01108 | SCR_011852 | 2026-08-01 12:04:32 | 37 |
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