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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 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Genome Annotation Generator Resource Report Resource Website 10+ mentions |
Genome Annotation Generator (RRID:SCR_016053) | GAG | data analysis software, data processing software, sequence analysis software, software application, software resource, source code | Command line program to read, modify, annotate and generate genomic data. Can write files to .gff3 or to the NCBI's .tbl format. | genome, annotation, tbl, ncbi, command, line, code, modify, read, annotate, gff3, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download | biotools:gag | https://bio.tools/gag | SCR_016053 | SciCrunch Registry | gag.py | 2026-10-17 01:29:20 | 18 | ||||||
|
Datamash Resource Report Resource Website 1+ mentions |
Datamash (RRID:SCR_016067) | data analysis software, data processing software, software application, software resource | Software for a command-line interface which performs basic numeric, textual and statistical operations on input textual data files. It is designed to aid researchers in automating analysis pipelines, without writing code or short scripts. | command-line, interface, basic, numerical, textual, statistical, operation, input, data, files, automate, analysis, pipelines | is listed by: Debian | Free Software Foundation (FSF) | Free, Available for download | https://sources.debian.org/src/datamash/ | SCR_016067 | SciCrunch Registry | GNU Datamash | 2026-10-17 01:29:20 | 4 | |||||||
|
Nanopolish Resource Report Resource Website 100+ mentions |
Nanopolish (RRID:SCR_016157) | data analysis software, data processing software, software application, software resource | Software package for signal-level analysis of Oxford Nanopore sequencing data. | Signal level analysis, Oxford Nanopore, sequencing data, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Free, Available for download, Freely available | OMICS_16545, biotools:nanopolish | https://bio.tools/nanopolish, https://sources.debian.org/src/nanopolish/ | SCR_016157 | SciCrunch Registry | 2026-10-17 01:29:09 | 477 | ||||||||
|
HiLive Resource Report Resource Website |
HiLive (RRID:SCR_016134) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for performing read mapping that maps Illumina HiSeq sequencer read alignments when they are produced. Used in Next Generation Sequencing in time critical, clinical applications. | perform, read, mapping, sequence, alignment, analysis, Illumina, time, critical, clinical, application |
is listed by: Debian is listed by: OMICtools |
the German Federal Ministry of Health IIA5-2512-FSB-725 | PMID:27794555 | Free, Available for download | OMICS_13393 | https://sources.debian.org/src/hilive/ | https://sourceforge.net/projects/hilive/ | SCR_016134 | SciCrunch Registry | 2026-10-17 01:29:04 | 0 | |||||
|
FSA Resource Report Resource Website 1+ mentions |
FSA (RRID:SCR_016114) | FSA | alignment software, data processing software, image analysis software, software application, software resource | Software for a statistical multiple sequence alignment algorithm which uses a "distance-based" approach to align homologous protein, RNA or DNA sequences. The GUI, MAD (Multiple Alignment Display), can display the intermediate alignments produced by FSA, where each character is colored according to the probability that it is correctly aligned. | multiple, sequence, alignment, algorithm, distance, approach, homologous, protein, DNA, RNA, acurate, fast |
is listed by: Debian is listed by: OMICtools has parent organization: University of California at Berkeley; Berkeley; USA |
PMID:19478997 | Free, available for download | https://sources.debian.org/src/fsa/ | SCR_016114 | SciCrunch Registry | Fast Statistical Alignment, FSA: Fast Statistical Alignment | 2026-10-17 01:29:21 | 3 | ||||||
|
GARLI Resource Report Resource Website 100+ mentions |
GARLI (RRID:SCR_016117) | GARLI | data analysis software, data processing software, software application, software resource | Software application for inferring phylogenetic trees and analysis of molecular sequence data using the maximum-likelihood criterion. It implements nucleotide, amino acid and codon-based models of sequence evolution. | inference, phylogenetic, tree, analysis, molecular, sequence, data, maximum, likelihood, criterion, nucleotide, amino acid, codon, model, evolution |
is listed by: Debian is listed by: OMICtools |
Free, Available for download, Freely available | OMICS_04234 | https://code.google.com/archive/p/garli/, https://sources.debian.org/src/garli/ | SCR_016117 | SciCrunch Registry | Genetic Algorithm for Rapid Likelihood Inference | 2026-10-17 01:29:04 | 280 | ||||||
|
Fsm-lite Resource Report Resource Website 10+ mentions |
Fsm-lite (RRID:SCR_016115) | data analysis software, data processing software, software application, software resource | Software application as a single-core implementation of frequency-based substring mining. It can be used in bioinformatics to extract substrings that discriminate two (or more) datasets inside high-throughput sequencing data. | protein, dna, rna, sequence, analysis, core, implementation, frequency, based, substring, mining, extract, discriminate, dataset, sequencing, high throughput |
is listed by: Debian is listed by: OMICtools |
Free, Available for download | OMICS_28406 | https://sources.debian.org/src/fsm-lite/ | SCR_016115 | SciCrunch Registry | fsm, Frequency-based String Mining, Frequency-based String Mining (lite) | 2026-10-17 01:29:01 | 19 | |||||||
|
gdpc Resource Report Resource Website |
gdpc (RRID:SCR_016119) | data processing software, data visualization software, software application, software resource | Software application for visualizing output data from molecular dynamics simulations. It can be customized to read almost any input file format, animate it, and output images of each frame. | visualizing, output, data, molecular, dynamic, simulation, animation, visualization |
is listed by: Debian is listed by: OMICtools |
Free, Available for download, Freely available | OMICS_19946 | https://sources.debian.org/src/gdpc/ | http://www.frantz.fi/software/gdpc.php, https://directory.fsf.org/wiki/Gdpc | SCR_016119 | SciCrunch Registry | 2026-10-17 01:29:01 | 0 | |||||||
|
GenomeTools Resource Report Resource Website 100+ mentions |
GenomeTools (RRID:SCR_016120) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software toolkit for biological sequence analysis and -presentation combined into a single binary. It is used for genome analysis, efficient processing of structured genome annotations and contains binaries for sequence and annotation handling, sequence compression, index structure generation and access, annotation visualization. | analysis, genome, annotate, sequence, compress, visualization, single, binary, combine, structure, efficient |
is listed by: Debian is listed by: OMICtools |
PMID:24091398 | Free, Available for download | OMICS_16119 | https://sources.debian.org/src/genometools/ | SCR_016120 | SciCrunch Registry | GenomeTool, Genome Tools, Genome Tool | 2026-10-17 01:29:08 | 150 | ||||||
|
bioSyntax Resource Report Resource Website 1+ mentions |
bioSyntax (RRID:SCR_016207) | data management software, software application, software resource | Software for syntax highlighting for computational biology. | computation, syntax, language, code, scientific, data, workflow, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
DOI:10.1186/s12859-018-2315-y | Free, Available for download | biotools:biosyntax, OMICS_25594 | https://github.com/bioSyntax/bioSyntax, https://bio.tools/biosyntax, https://sources.debian.org/src/biosyntax/ | SCR_016207 | SciCrunch Registry | 2026-10-17 01:29:02 | 2 | |||||||
|
IDEPI - IDentify EPItopes Resource Report Resource Website |
IDEPI - IDentify EPItopes (RRID:SCR_016171) | software library, software resource, software toolkit | IDEPI is a domain-specific and extensible software library for supervised learning of models that relate genotype to phenotype for HIV-1 and other organisms. IDEPI makes use of open source libraries for machine learning (scikit- learn, scikit-learn.org/), sequence alignment (HMMER, hmmer.janelia.org/), sequence manipulation (BioPython, biopython.org), and parallelization (joblib, pythonhosted.org/joblib), and provides a programming interface to allow the users to engineer sequence features and select machine learning algorithms appropriate for their application. | modeling, machine, learning, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:25254639 | Free, Available for download | biotools:idepi | https://bio.tools/idepi | SCR_016171 | SciCrunch Registry | 2026-10-17 01:29:22 | 0 | |||||||
|
odMLtables Resource Report Resource Website 1+ mentions |
odMLtables (RRID:SCR_016228) | data management software, data processing software, data visualization software, software application, software resource | Software that facilitates the handling of metadata collections stored in the odML format. Some supported operations include reduction, merging of odml structures, and the conversion from the hierarchical odML format to tabular formats. | metadata, collection, odml, hierarchy, tabular structure, markup language, data management, graph, spreadsheet, bio.tools |
uses: Open metadata mark up language is listed by: Debian is listed by: bio.tools |
PMID:31611781 | Free, Available for download, Tutorial available | biotools:odMLtables | https://github.com/INM-6/python-odmltables, https://bio.tools/odMLtables | SCR_016228 | SciCrunch Registry | odML-tables, odML tables | 2026-10-17 01:29:02 | 2 | ||||||
|
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 | 2026-10-17 01:28:35 | 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 | 2026-10-17 01:28:35 | 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 | 2026-10-17 01:28:21 | 87 | |||||||
|
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 | 2026-10-17 01:28:21 | 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 | 2026-10-17 01:27:47 | 7088 | |||||
|
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 | 2026-10-17 01:28:10 | 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 | 2026-10-17 01:28:24 | 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 | 2026-10-17 01:27:50 | 11 |
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