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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MentaLiST Resource Report Resource Website 1+ mentions |
MentaLiST (RRID:SCR_016469) | software application, sequence analysis software, data processing software, software resource, data analysis software | Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes. | next, generation, sequencing, multi, locus, sequence, typing, pathogen, surveillance, gene, identify, strain, type, housekeeping, whole, genome, sequencing, data, bacteria, genotyping, bio.tools |
is listed by: bio.tools is listed by: Debian |
Canadian Institute for Health Research ; Genome Canada ; Genome BC |
PMID:29319471 | Free, Available for download, Freely available | biotools:mentalist | https://bio.tools/mentalist | SCR_016469 | 2026-02-15 09:21:52 | 8 | ||||||
|
fermi Resource Report Resource Website |
fermi (RRID:SCR_016652) | software application, sequence analysis software, data processing software, software resource, data analysis software | Software assembler and analysis tool for whole-genome short-gun sequencing for Illumina reads. Provides tools for error correction, sequence-to-read alignment and comparison between read sets. Used for large genomes. | assembler, analysis, whole, genome, short, gun, sequencing, error, correction | is listed by: OMICtools | NHGRI U01 HG005208 | PMID:22569178 | Free, Available for download, Freely available | SCR_016652 | 2026-02-15 09:21:45 | 0 | ||||||||
|
CheckM Resource Report Resource Website 100+ mentions |
CheckM (RRID:SCR_016646) | software application, data processing software, software resource, software toolkit, data analysis software | Software tool to assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes by using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. | assess, quality, microbial, genome, recovered, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/gr.186072.114 | Free, Available for download, Freely available | biotools:checkm | https://github.com/Ecogenomics/CheckM https://bio.tools/checkm |
SCR_016646 | 2026-02-15 09:21:45 | 184 | |||||||
|
KAT Resource Report Resource Website 10+ mentions |
KAT (RRID:SCR_016741) | KAT | software application, data processing software, software resource, software toolkit, data analysis software | Software that generates, analyses and compares k-mer spectra produced from sequence files. Used to quality control NGS datasets and genome assemblies. | generate, analyse, compare, k-mer, spectra, sequence, file, quality, control, NGS, dataset, genome, assembly, bio.tools |
is listed by: Debian is listed by: bio.tools |
BBSRC | DOI:10.1093/bioinformatics/btw663 | Free, Available for download, Freely available | biotools:kat | http://www.earlham.ac.uk/kat-tools https://bio.tools/kat |
SCR_016741 | K-mer Analysis Toolkit | 2026-02-15 09:21:48 | 19 | ||||
|
Flye Resource Report Resource Website 100+ mentions |
Flye (RRID:SCR_017016) | software application, sequence analysis software, data processing software, software resource, software toolkit, data analysis software | Software package as de novo assembler for single molecule sequencing reads. Used for assembling long, error prone reads such as those produced by PacBio and Oxford Nanopore Technologies, for fast and accurate genome reconstructions. Available for Linux and MacOS platforms. | assembler, single, molecule, sequencing, long, error, read, fast, accurate, genome, reconstruction, nucleotide, quality, data, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of California at San Diego; California; USA |
PMID:27956617 | Free, Available for download, Freely available | biotools:Flye | https://bio.tools/Flye https://sources.debian.org/src/flye/ |
SCR_017016 | 2026-02-15 09:21:57 | 267 | |||||||
|
BBmap Resource Report Resource Website 500+ mentions |
BBmap (RRID:SCR_016965) | software application, data processing software, software resource, alignment software, image analysis software, software toolkit | Software tool as a short read aligner for DNA and RNA seq data. Used for large genomes with millions of scaffolds. Can align reads from Illumina, PacBio, 454, Sanger, Ion Torrent, Nanopore. Fast and accurate, particularly with highly mutated genomes or reads with long indels, even whole gene deletions over 100kbp long. It has no upper limit to genome size or number of contigs. Written in Java, can run on any platform. | Joint Genome Institute, short, read, aligner, DNA, RNA, sequencing, data, large, genome, scaffold, mutated, long, indel |
is listed by: Bestus Bioinformaticus Tools is listed by: Debian is related to: University of California at Berkeley; Berkeley; USA |
Free, Available for download, Freely available | https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmap-guide/ https://sources.debian.org/src/bbmap/ |
SCR_016965 | 2026-02-15 09:21:52 | 797 | |||||||||
|
TopDom Resource Report Resource Website 10+ mentions |
TopDom (RRID:SCR_016964) | TOPDOM | software application, data processing software, software resource, software toolkit, data analysis software | Software tool to identify Topological Domains, which are basic builiding blocks of genome structure. Detects topological domains in a linear time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | identify, topological, domain, genome, structure, linear, time, data, analysis |
has parent organization: University of Southern California; Los Angeles; USA works with: CCTOP |
NHLBI U01 HL108634; NIDDK U54 DK107981; NSF CAREER 0747475; NSF CAREER 1150287; Arnold and Mabel Beckman foundation ; Pew Charitable Trusts |
PMID:26704975 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016964 | TOPological DOMains, Topological Domains, TopDom_v0.0.2, TopDom_v0.0.1 | 2026-02-15 09:21:12 | 10 | ||||||
|
Maize Database of Images and Genomes Resource Report Resource Website 1+ mentions |
Maize Database of Images and Genomes (RRID:SCR_016987) | MaizeDIG | database, service resource, production service resource, data or information resource, analysis service resource | Genotype and phenotype database for maize images based on BioDIG. Supports multiple reference genomes and has been integrated with the MaizeGDB Genome Browser to make custom tracks showing mutant phenotypes within their genomic context. Allows for custom tagging of images to highlight regions related to the phenotypes. This is accomplished through an interface allowing users to create links from images to genomic coordinates and to curate and search images by gene model ID, gene symbol, and gene name. | genotype, phenotype, collection, maize, image, reference, genome | works with: MaizeGDB | Free, Freely available | SCR_016987 | Maize Dig, MaizeDatabase of Images and Genomes, MaizeDig, MaizeDIG | 2026-02-15 09:21:53 | 5 | ||||||||
|
SwiftOrtho Resource Report Resource Website 1+ mentions |
SwiftOrtho (RRID:SCR_017122) | software application, data processing software, data analysis software, software resource | Software tool for orthology analysis to identify orthologs, paralogs and co orthologs for genomes. Used to perform homology classification across genomes of different species in large genomic datasets. | orthology, analysis, identify, ortholog, paralog, co ortholog, genome, homology, different, species, large, dataset, bio.tools |
uses: Python Programming Language is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/543223 | Free, Available for download, Freely available | OMICS_30890, biotools:SwiftOrtho | https://bio.tools/SwiftOrtho | SCR_017122 | 2026-02-15 09:21:56 | 4 | |||||||
|
dndSCV Resource Report Resource Website 10+ mentions |
dndSCV (RRID:SCR_017093) | software application, data processing software, data analysis software, software resource | Software R package as suite of dN/dS methods to quantify selection in cancer and somatic evolution. Contains functions to quantify dN/dS ratios for missense, nonsense and essential splice mutations, at level of individual genes, groups of genes or at whole genome level. Used to detect cancer driver genes on datasets. | dN/dS, method, quantify, selection, cancer, somatic, evolution, missense, nonsense, essential, splice, mutation, gene, genome, dataset |
uses: devtools is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_017093 | 2026-02-15 09:21:15 | 35 | ||||||||||
|
WTDBG Resource Report Resource Website 50+ mentions |
WTDBG (RRID:SCR_017225) | software application, sequence analysis software, data processing software, software resource, alignment software, image analysis software, data analysis software | Software tool as de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies. It assembles raw reads without error correction and then builds consensus from intermediate assembly output. Desiged to assemble huge genomes in very limited time. | sequence, assembler, de novo, long, noisy, read, likelihood, estimator, genome |
is listed by: OMICtools is listed by: Debian |
NSFC ; NHGRI R01 HG010040 |
PMID:31819265 | Free, Available for download, Freely available | OMICS_24025 | https://github.com/ruanjue/wtdbg https://sources.debian.org/src/wtdbg2/ |
SCR_017225 | Wtdbg2, wtdgb, Wtdgb, wtdgb2 | 2026-02-15 09:22:00 | 57 | |||||
|
3D de novo assembly Resource Report Resource Website 10+ mentions |
3D de novo assembly (RRID:SCR_017227) | software application, data processing software, data analysis software, software resource | Software tool as 3D de novo assembly (3D DNA) pipeline. Used to help generate HI-C assembly. | de novo, assembly, 3D, DNA, HI-C, data, scaffold, pipeline, chromosome, genome | DOI:10.1126/science.aal3327 | Free, Available for download, Freely available | SCR_017227 | 2026-02-15 09:21:17 | 40 | ||||||||||
|
matemaker Resource Report Resource Website 1+ mentions |
matemaker (RRID:SCR_017199) | software application, sequence analysis software, data processing software, software resource, standalone software, data analysis software | Software tool to make artificial mate pairs from long sequences for scaffolding. | artificial, mate, pair, long, sequence, scaffolding, genomics, genome, assembly | Free, Available for download, Freely available | SCR_017199 | matemaker v1.0.0 | 2026-02-15 09:21:59 | 4 | ||||||||||
|
RNAmmer Resource Report Resource Website 100+ mentions |
RNAmmer (RRID:SCR_017075) | software application, data analysis service, data processing software, software resource, data access protocol, web service, service resource, standalone software, production service resource, analysis service resource, data analysis software | Software package to predict ribosomal RNA genes in full genome sequences by utilising two levels of Hidden Markov Models. Consistent and rapid annotation of ribosomal RNA genes. | predict, ribosomal, RNA, gene, full, genome, sequence, HMM, rRNA | has parent organization: Technical University of Denmark; Lyngby; Denmark | EMBIO at the University of Oslo ; Research Council of Norway ; Danish Center for Scientific Computing ; European Union |
PMID:17452365 | Restricted | SCR_017075 | 2026-02-15 09:21:14 | 103 | ||||||||
|
phyloscanner Resource Report Resource Website 1+ mentions |
phyloscanner (RRID:SCR_017400) | software application, data processing software, data analysis software, software resource | Software tool for analysing pathogen genetic diversity and relationships between and within hosts at once, in windows along genome. Inferring transmission from within and between host pathogen genetic diversity. | Analysing, pathogen, genetic, diversity, relationship, host, genome | ERC Advanced Grant ; Bill & Melinda Gates Foundation ; Medical Research Council |
PMID:29186559 | Free, Available for download, Freely available | SCR_017400 | 2026-02-15 09:22:04 | 1 | |||||||||
|
PILER Resource Report Resource Website 10+ mentions |
PILER (RRID:SCR_017333) | software application, data processing software, data analysis software, software resource | Software tool for analyzing repetitive DNA found in genome sequences. Software package for identification and classification of genomic repeats. Used for identifying patterns of local alignments induced by certain classes of repeats. | analysis, repetitive, DNA, genome, sequence, classification, alignment | is listed by: OMICtools | PMID:15961452 | Free, Available for download, Freely available | https://omictools.com/piler-tool | SCR_017333 | 2026-02-15 09:22:01 | 15 | ||||||||
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MCScan Resource Report Resource Website 10+ mentions |
MCScan (RRID:SCR_017650) | software application, sequence analysis software, data processing software, software resource, software toolkit, data analysis software | Software package to simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors.Used to identify conserved gene arrays both within same genome and across different genomes. Command line program to wrap dagchainer and combine pairwise results into multi alignments in column format. | Simultaneously, scan, multiple, genome, identify, homologous, chromosomal, region, align, gene, anchor, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Georgia; Georgia; USA |
Free, Available for downoad, Freely available | biotools:MCScan | http://chibba.agtec.uga.edu/duplication/mcscan/ https://bio.tools/MCScan |
SCR_017650 | Multiple Collinearity Scan | 2026-02-15 09:22:04 | 37 | |||||||
|
Blobtools Resource Report Resource Website 100+ mentions |
Blobtools (RRID:SCR_017618) | software application, data visualization software, data processing software, software resource, data analytics software | Software tool as modular command line solution for visualisation, quality control and taxonomic partitioning of genome datasets. Used for interrogation of genome assemblies. Assists in primary partitioning of data, leading to improved assemblies, and screening of final assemblies for potential contaminants. | Modular, command, line, solution, visualisation, quality, control, taxonomic, partitioning, genome, dataset, genome assembly, screening, contaminant, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: BlobTools2 |
James Hutton Institute/Edinburgh University School of Biological Sciences fellowship ; BBSRC |
DOI:10.12688/f1000research.12232.1 | Free, Available for download, Freely available | biotools:blobtools | https://github.com/DRL/blobtools https://bio.tools/blobtools |
SCR_017618 | BlobTools | 2026-02-15 09:22:10 | 199 | |||||
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Ngmlr Resource Report Resource Website 10+ mentions |
Ngmlr (RRID:SCR_017620) | NGMLR | software application, data processing software, software resource, alignment software, image analysis software | Software tool as long read mapper designed to align PacBio or Oxford Nanopore reads to reference genome and optimized for structural variation detection. | Long, read, mapper, align, PacBio, Oxford Nanopore, read, reference, genome, structural, variantion, detection, bio.tools |
is listed by: bio.tools is listed by: Debian |
National Science Foundation ; NHGRI R01 HG006677; NHGRI UM1 HG008898 |
PMID:29713083 | Free, Available for download, Freely available | biotools:ngmlr | https://bio.tools/ngmlr | SCR_017620 | coNvex Gap-cost alignMent for Long Reads | 2026-02-15 09:22:04 | 31 | ||||
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TCGAbiolinks Resource Report Resource Website 50+ mentions |
TCGAbiolinks (RRID:SCR_017683) | software application, data processing software, data analysis software, software resource | Software R Bioconductor package for integrative analysis with TCGA data.TCGAbiolinks is able to access National Cancer Institute Genomic Data Commons thorough its GDC Application Programming Interface to search, download and prepare relevant data for analysis in R. | Integrative, analysis, TCGA data, cancer, genome, atlas, genomic, analysis, expression, methylated, region, survival plot, phenotype, tumor, epigenomic, alteration, clinical, molecular, retrival | BridgeIRIS ; INNOVIRIS ; Region de Bruxelles Capitale ; Brussels ; Belgium ; GENGISCAN ; São Paulo Research Foundation |
PMID:26704973 DOI:10.12688/f1000research.8923.2 |
Free, Available for download, Freely available | https://github.com/BioinformaticsFMRP/TCGAbiolinks | SCR_017683 | Cancer Genome Atlas (TCGA) biolinks | 2026-02-15 09:22:06 | 93 |
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