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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 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
GNomEx Resource Report Resource Website 1+ mentions |
GNomEx (RRID:SCR_011805) | GNomEx | data repository, service resource, storage service resource | A Genomic Laboratory Information Management System (LIMS) and Data repository that can function as an experiment tracking and workflow management system for Core Facilities as well as an advanced data repository for storing and sharing genomic data sets. |
is listed by: OMICtools has parent organization: University of Utah; Utah; USA |
PMID:20828407 | OMICS_01005 | https://uofuhealth.utah.edu/huntsman/shared-resources/gba/bioinformatics/software/ | http://hci-scrum.hci.utah.edu/gnomexdoc/ | SCR_011805 | SciCrunch Registry | 2026-10-24 12:46:40 | 5 | |||||||
|
Infernal Resource Report Resource Website 500+ mentions |
Infernal (RRID:SCR_011809) | Infernal | software resource | Software for searching DNA sequence databases for RNA structure and sequence similarities. | FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: ANNOgesic has parent organization: Janelia Research |
PMID:24008419 DOI:10.1093/bioinformatics/btp157 |
GNU General Public License, v3 | OMICS_00977 | https://sources.debian.org/src/infernal/ | SCR_011809 | SciCrunch Registry | Infernal: inference of RNA alignments, INFERence of RNA Alignment | 2026-10-24 12:46:40 | 772 | |||||
|
GenomeMatcher Resource Report Resource Website 50+ mentions |
GenomeMatcher (RRID:SCR_011800) | GenomeMatcher | software resource | A graphical interface for comparative genomics. | is listed by: OMICtools | OMICS_00936 | SCR_011800 | SciCrunch Registry | 2026-10-24 12:46:40 | 65 | ||||||||||
|
GenomeRing Resource Report Resource Website 1+ mentions |
GenomeRing (RRID:SCR_011801) | GenomeRing | software resource | Alignment visualization based on SuperGenome coordinates. |
is listed by: OMICtools has parent organization: University of Tubingen; Tubingen; Germany |
OMICS_00937 | SCR_011801 | SciCrunch Registry | 2026-10-24 12:46:40 | 2 | ||||||||||
|
Gobe Resource Report Resource Website 1+ mentions |
Gobe (RRID:SCR_011802) | Gobe | software resource | An interactive, web-based tool for comparative genomic visualization. | is listed by: OMICtools | OMICS_00938 | SCR_011802 | SciCrunch Registry | 2026-10-24 12:46:40 | 2 | ||||||||||
|
GSV Resource Report Resource Website 1+ mentions |
GSV (RRID:SCR_011803) | GSV | software resource | Software that allows users to upload files which contain synteny regions between two or more genomes and interactively visualize the synteny between them. | is listed by: OMICtools | OMICS_00939 | SCR_011803 | SciCrunch Registry | Genome Synteny Viewer | 2026-10-24 12:46:40 | 2 | |||||||||
|
NextGENe Resource Report Resource Website 100+ mentions |
NextGENe (RRID:SCR_011859) | NextGENe | data analysis software, data processing software, software application, software resource | Software tool for Next Generation sequence analysis. Analytical partner for analysis of desktop sequencing data produced by Illumina iSeq, Miniseq, MiSeq, NextSeq, HiSeq, and NovaSeq systems, Ion Torrent Ion GeneStudio S5, PGM, and Proton systems as well as other platforms. Software runs on Windows Operating System, which provides biologist friendly interface. It does not require scripting or other bioinformatics support. | Next Generation Sequence Analysis, desktop sequencing data analysis, sequencing data | is listed by: OMICtools | Commercial license | OMICS_01131 | http://softgenetics.com/NextGENe.html | SCR_011859 | SciCrunch Registry | Next GENeration Sequence Analysis | 2026-10-24 12:46:41 | 381 | ||||||
|
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 | SciCrunch Registry | 2026-10-24 12:46:41 | 37 | ||||||||||
|
NARWHAL Resource Report Resource Website 10+ mentions |
NARWHAL (RRID:SCR_011858) | NARWHAL | software resource | Automates the primary analysis of massive parallel sequencing data. |
is listed by: OMICtools has parent organization: Netherlands Bioinformatics Centre |
OMICS_01130 | SCR_011858 | SciCrunch Registry | 2026-10-24 12:46:41 | 10 | ||||||||||
|
UTGB Toolkit Resource Report Resource Website 1+ mentions |
UTGB Toolkit (RRID:SCR_011797) | UTGB Toolkit | software resource | An open-source software for developing personalized genome browsers that work in web browsers. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tokyo; Tokyo; Japan |
Open unspecified license | OMICS_00927, biotools:utgb_toolkit | https://bio.tools/utgb_toolkit | SCR_011797 | SciCrunch Registry | University of Tokyo Genome Browser | 2026-10-24 12:46:40 | 1 | ||||||
|
AdapterRemoval Resource Report Resource Website 500+ mentions |
AdapterRemoval (RRID:SCR_011834) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software program to remove residual adapter sequences from next generation sequencing reads. Used for cleaning of next-generation sequencing reads. AdapterRemoval v2 introduces improvements in throughput, through use of single instruction, multiple data (SIMD; SSE1 and SSE2) instructions and multi-threading support; handles datasets containing reads or read-pairs with different adapters or adapter pairs; provides simultaneous demultiplexing and adapter trimming; has ability to reconstruct adapter sequences from paired-end reads for poorly documented data sets; provides native gzip and bzip2 support. | cleaning of next-generation sequencing reads, remove residual adapter sequences, adapter, sequence, residual, next generation sequencing reads, |
is listed by: OMICtools is listed by: Debian |
Danish Council for Independent Research ; Danish National Research Foundation ; Lundbeck Foundation Grant ; Marie Curie International Outgoing Fellowship within the 7th European Community Framework Programme |
PMID:22748135 PMID:26868221 DOI:10.1186/s13104-016-1900-2 |
Free, Available for download, Freely available | OMICS_01081 | https://sources.debian.org/src/adapterremoval/ | http://code.google.com/p/adapterremoval/, https://github.com/slindgreen/AdapterRemoval, https://sources.debian.org/src/adapterremoval/ | SCR_011834 | SciCrunch Registry | AdapterRemoval v2 | 2026-10-24 12:46:40 | 773 | ||||
|
Btrim Resource Report Resource Website 50+ mentions |
Btrim (RRID:SCR_011836) | Btrim | software resource | A fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Yale School of Medicine; Connecticut; USA |
PMID:21651976 | biotools:btrim, OMICS_01083 | https://bio.tools/btrim | SCR_011836 | SciCrunch Registry | 2026-10-24 12:46:40 | 87 | |||||||
|
Coral Resource Report Resource Website 100+ mentions |
Coral (RRID:SCR_011849) | Coral | software resource | An error correction algorithm for correcting reads from DNA sequencing platforms such as the Illumina Genome Analyzer or HiSeq platforms or Roche/454 Genome Sequencer. |
is listed by: OMICtools has parent organization: University of Helsinki; Helsinki; Finland |
PMID:21471014 | OMICS_01099 | SCR_011849 | SciCrunch Registry | 2026-10-24 12:46:41 | 210 | |||||||||
|
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 |
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