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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
QuorUM Resource Report Resource Website 10+ mentions |
QuorUM (RRID:SCR_011840) | QuorUM | software resource | Software tool as error corrector for Illumina reads. It is distributed and used with MaSuRCA, or it can be used independently. |
is listed by: OMICtools is listed by: Debian has parent organization: University of Maryland; Maryland; USA |
DOI:10.1371/journal.pone.0130821 | OMICS_01107 | https://sources.debian.org/src/quorum/ | SCR_011840 | SciCrunch Registry | 2026-10-24 12:46:41 | 32 | ||||||||
|
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 | SciCrunch Registry | 2026-10-24 12:46:41 | 7088 | |||||
|
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 | SciCrunch Registry | 2026-10-24 12:46:43 | 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 | SciCrunch Registry | 2026-10-24 12:46:43 | 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 | SciCrunch Registry | 2026-10-24 12:46:43 | 7 | ||||||||
|
Glimmer Resource Report Resource Website 500+ mentions |
Glimmer (RRID:SCR_011931) | Glimmer | analysis service resource, data analysis service, production service resource, service resource, software 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 | SciCrunch Registry | Glimmer - Microbial Gene-Finding System | 2026-10-24 12:46:42 | 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 | SciCrunch Registry | 2026-10-24 12:46:43 | 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 | SciCrunch Registry | MetaVelvet: a short read assember for metagenomics | 2026-10-24 12:46:42 | 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 | SciCrunch Registry | 2026-10-24 12:46:42 | 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 | SciCrunch Registry | 2026-10-24 12:46:41 | 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 | SciCrunch Registry | 2026-10-24 12:46:41 | 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 | SciCrunch Registry | GeneStitch: Network Matching Algorithm to Gene Assembly | 2026-10-24 12:46:42 | 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 | SciCrunch Registry | 2026-10-24 12:46:41 | 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 | SciCrunch Registry | Genovo - Metagenomic de novo Sequencing | 2026-10-24 12:46:42 | 227 | |||||||||
|
AACC Resource Report Resource Website 100+ mentions |
AACC (RRID:SCR_011999) | AACC | community building portal, data or information resource, portal | An international society comprised of medical professionals with an interest in clinical chemistry, clinical laboratory science, and laboratory medicine. | is listed by: OMICtools | OMICS_01788 | SCR_011999 | SciCrunch Registry | American Association for Clinical Chemistry | 2026-10-24 12:46:43 | 264 | |||||||||
|
METAREP Resource Report Resource Website 1+ mentions |
METAREP (RRID:SCR_011926) | METAREP | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | 2026-10-24 12:46:42 | 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 | SciCrunch Registry | 2026-10-24 12:46:41 | 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 | SciCrunch Registry | 2026-10-24 12:46:41 | 2 | |||||||||
|
Globus Genomics Resource Report Resource Website 10+ mentions |
Globus Genomics (RRID:SCR_011887) | Globus Genomics | data repository, service resource, storage 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 | SciCrunch Registry | 2026-10-24 12:46:41 | 26 | |||||||||
|
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 | SciCrunch Registry | 2026-10-24 12:46:42 | 281 |
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