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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BlobTools2 Resource Report Resource Website 100+ mentions |
BlobTools2 (RRID:SCR_023351) | software application, data processing software, data analysis software, software resource | Software suite for identifying and isolating non-target data in draft and publicly available genome assemblies. Used to process assembly, read and analysis files for fully reproducible interactive exploration in browser-based Viewer. Used for interactive quality assessment of genome assemblies .BlobTools2 is reimplementation of BlobTools, written in Python 3 with fully modular design to make creating new datasets and adding additional analysis types easier. | interactive quality assessment, genome assemblies, identifying and isolating non-target data, genome, QC, filtering, process assembly, read and analysis files, |
is related to: Blobtools is related to: Blobtoolkit |
BBSRC Bioinformatics and Biological Resources fund | PMID:32071071 | Free, Available for download, Freely available | https://github.com/blobtoolkit/blobtoolkit | SCR_023351 | blobtoolkit | 2026-02-15 09:22:26 | 382 | ||||||
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CRISPOR Resource Report Resource Website 1000+ mentions |
CRISPOR (RRID:SCR_015935) | web application, software resource | Web application that helps design, evaluate and clone guide sequences for the CRISPR/Cas9 system. This sgRNA design tool assists with guide selection in a variety of genomes and pre-calculated results for all human coding exons as a UCSC Genome Browser track. | rna, sg, sgrna, crispr, genome, off-target, prediction, accuracy, clone, cas9, coding, exon | is related to: UCSC Genome Browser | MRC 53658; NIH Office of the Director U42 OD011174; NHGRI U41 HG002371; NCI U54 HG007990; California Institute of Regenerative Medicine GC1R-06673C; Agence Nationale pour la Recherche ; Fondation pour la Recherche Médicale DEQ20140329544 |
PMID:27380939 | Free, Available for download | https://github.com/maximilianh/crisporWebsite | SCR_015935 | 2026-02-15 09:21:28 | 1320 | |||||||
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loadBAM2ge_db Resource Report Resource Website 1+ mentions |
loadBAM2ge_db (RRID:SCR_015951) | software application, data visualization software, data processing software, software resource | Software pipeline that visualizes mapping results (in BAM format) on Genome Explorer. | bam, map, mapping, genome, pipeline, maser, visualization, explorer | Public | SCR_015951 | loadBAM2ge_db (PE) | 2026-02-15 09:20:59 | 1 | ||||||||||
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NBDC - National Bioscience Database Center Resource Report Resource Website 1+ mentions |
NBDC - National Bioscience Database Center (RRID:SCR_000814) | NBDC | organization portal, data or information resource, database, portal | The National Bioscience Database Center (NBDC) intends to integrate all databases for life sciences in Japan, by linking each database with expediency to maximize convenience and make the entire system more user-friendly. We aim to focus our attention on the needs of the users of these databases who have all too often been neglected in the past, rather than the needs of the people tasked with the creation of databases. It is important to note that we will continue to honor the independent integrity of each database that will contribute to our endeavor, as we are fully aware that each database was originally crafted for specific purposes and divergent goals. Services: * Database Catalog - A catalog of life science related databases constructed in Japan that are also available in English. Information such as URL, status of the database site (active vs. inactive), database provider, type of data and subjects of the study are contained for each database record. * Life Science Database Cross Search - A service for simultaneous searching across scattered life-science databases, ranging from molecular data to patents and literature. * Life Science Database Archive - maintains and stores the datasets generated by life scientists in Japan in a long-term and stable state as national public goods. The Archive makes it easier for many people to search datasets by metadata in a unified format, and to access and download the datasets with clear terms of use. * Taxonomy Icon - A collection of icons (illustrations) of biological species that is free to use and distribute. There are more than 200 icons of various species including Bacteria, Fungi, Protista, Plantae and Animalia. * GenLibi (Gene Linker to bibliography) - an integrated database of human, mouse and rat genes that includes automatically integrated gene, protein, polymorphism, pathway, phenotype, ortholog/protein sequence information, and manually curated gene function and gene-related or co-occurred Disease/Phenotype and bibliography information. * Allie - A search service for abbreviations and long forms utilized in life sciences. It provides a solution to the issue that many abbreviations are used in the literature, and polysemous or synonymous abbreviations appear frequently, making it difficult to read and understand scientific papers that are not relevant to the reader's expertise. * inMeXes - A search service for English expressions (multiple words) that appear no less than 10 times in PubMed/MEDLINE titles or abstracts. In addition, you can easily access the sentences where the expression was used or other related information by clicking one of the search results. * HOWDY - (Human Organized Whole genome Database) is a database system for retrieving human genome information from 14 public databases by using official symbols and aliases. The information is daily updated by extracting data automatically from the genetic databases and shown with all data having the identifiers in common and linking to one another. * MDeR (the MetaData Element Repository in life sciences) - a web-based tool designed to let you search, compare and view Data Elements. MDeR is based on the ISO/IEC 11179 Part3 (Registry metamodel and basic attributes). * Human Genome Variation Database - A database for accumulating all kinds of human genome variations detected by various experimental techniques. * MEDALS - A portal site that provides information about databases, analysis tools, and the relevant projects, that were conducted with the financial support from the Ministry of Economy, Trade and Industry of Japan. | life science, research, database, catalog, tool, gene, service, molecule, patent, literature, taxonomy, image, bacteria, fungus, protist, plant, animal, human, mouse, rat, gene, protein, polymorphism, pathway, phenotype, ortholog, protein sequence, gene function, disease, phenotype, bibliography, english expression, human genome, genome, human genome variation, variation, analysis tool |
has parent organization: Japan Science and Technology Agency is parent organization of: Human Variation DB is parent organization of: Japanese Genotype-phenotype Archive (JGA) is parent organization of: ChIP-Atlas |
Japan Science and Technology Agency | nlx_151485 | SCR_000814 | National Bioscience Database Center, National Bioscience Database Center (NBDC) | 2026-02-15 09:17:59 | 3 | |||||||
|
SPAdes Resource Report Resource Website 100+ mentions |
SPAdes (RRID:SCR_000131) | SPAdes | software toolkit, software resource | Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | assembler, single, cell, small, genome, short, read, data |
is used by: shovill is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: rnaSPAdes is related to: rnaQUAST has parent organization: Saint Petersburg Academic University; Saint Petersburg; Russia works with: Illumina iSeq 100 Sequencing System |
Government of the Russian Federation ; NCRR P41 RR024851 |
PMID:24093227 PMID:22506599 DOI:10.1089/cmb.2012.0021 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01502 | https://sources.debian.org/src/spades/ | http://bioinf.spbau.ru/spades/ | SCR_000131 | SPAdes Genome Assembler | 2026-02-15 09:17:52 | 101 | |||
|
International Gene Trap Consortium Resource Report Resource Website 10+ mentions |
International Gene Trap Consortium (RRID:SCR_002305) | IGTC | material resource, cell repository, biomaterial supply resource | Consortium represents all publicly available gene trap cell lines, which are available on non-collaborative basis for nominal handling fees. Researchers can search and browse IGTC database for cell lines of interest using accession numbers or IDs, keywords, sequence data, tissue expression profiles and biological pathways, can find trapped genes of interest on IGTC website, and order cell lines for generation of mutant mice through blastocyst injection. Consortium members include: BayGenomics (USA), Centre for Modelling Human Disease (Toronto, Canada), Embryonic Stem Cell Database (University of Manitoba, Canada), Exchangeable Gene Trap Clones (Kumamoto University, Japan), German Gene Trap Consortium provider (Germany), Sanger Institute Gene Trap Resource (Cambridge, UK), Soriano Lab Gene Trap Resource (Mount Sinai School of Medicine, New York, USA), Texas Institute for Genomic Medicine - TIGM (USA), TIGEM-IRBM Gene Trap (Naples, Italy). | embryo, embryonic, gene, genome, allele, analysis, assay, bioinformatics, blastocyst, cell, colony, consortium, genotyping, hybridization, in situ, international, knockout, murine, mutant, mutation, probe, qpcr, researcher, scientist, sequence, stem cell, tagging, trap, vector, cell line, embryonic stem cell line, FASEB list |
is listed by: One Mind Biospecimen Bank Listing is related to: Centre for Modeling Human Disease Gene Trap Resource has parent organization: University of California at San Francisco; California; USA is parent organization of: International Gene Trap Consortium Pathways |
NCRR P41 RR01081 | PMID:16381950 | Restricted | nif-0000-00036 | https://igtc.org/ | SCR_002305 | International Gene Trap Consortium | 2026-02-15 09:18:16 | 43 | ||||
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Genetic Association Information Network (GAIN) Resource Report Resource Website 1+ mentions |
Genetic Association Information Network (GAIN) (RRID:SCR_013703) | GAIN | organization portal, data or information resource, consortium, portal | The Genetic Association Information Network (GAIN) supports a series of Genome-Wide Association Studies (GWAS) designed to identify specific points of DNA variation associated with the occurrence of a particular common disease. Initially focusing on six major common diseases, GAIN focused on combining the results with clinical data to create a significant new resource for genetic researchers. | tool development, biomarker research, data-sharing enabler, genome, genome wide association studies, FNIH, | has parent organization: Foundation for the National Institutes of Health | Pfizer Inc ; Affymetrix Inc |
SCR_013703 | 2026-02-15 09:20:51 | 9 | |||||||||
|
RAST Server Resource Report Resource Website 500+ mentions |
RAST Server (RRID:SCR_014606) | RAST | service resource, production service resource | A SEED-quality automated service that annotates complete or nearly complete bacterial and archaeal genomes across the entire phylogenetic tree. RAST can also be used to analyze draft genomes. | microbiome, seed, annotate, genome, bacteria, archaea, service, bio.tools |
is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools |
National Science Foundation 0850546; NIAID contract HHSN272200900040C |
PMID:18261238 | Free for the scientific community, Login required | biotools:theseed | https://bio.tools/theseed | SCR_014606 | Rapid Annotation using Subsystem Technology, Rapid Annotation using Subsystem Technology Server | 2026-02-15 09:21:06 | 907 | ||||
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Prokka Resource Report Resource Website 1000+ mentions |
Prokka (RRID:SCR_014732) | software application, sequence analysis software, data processing software, software resource, data analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for the rapid annotation of prokaryotic genomes. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | annotation, prokaryote, genome, prokaryotic genome, sequence analysis software, annotation software, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1093/bioinformatics/btu153 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04220, biotools:prokka | https://bio.tools/prokka https://sources.debian.org/src/prokka/ https://sources.debian.org/src/prokka/ |
SCR_014732 | 2026-02-15 09:20:45 | 4876 | |||||||
|
TransDecoder Resource Report Resource Website 1000+ mentions |
TransDecoder (RRID:SCR_017647) | software application, standalone software, data processing software, software resource | Software tool to identify candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV. | Identify, candidate, coding, region, transcript, sequence, de novo, RNAseq, assembly, alignment, genome, open, reading, frame, homology, protein, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:transDecoder, OMICS_10852 | https://bio.tools/TransDecoder https://sources.debian.org/src/transdecoder/ https://github.com/TransDecoder/TransDecoder/wiki |
SCR_017647 | , Find Coding Regions Within Transcripts | 2026-02-15 09:22:11 | 1309 | |||||||
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LACHESIS Resource Report Resource Website 50+ mentions |
LACHESIS (RRID:SCR_017644) | software application, data processing software, software resource | Software tool for chromosome scale scaffolding of de novo genome assemblies based on chromatin interactions.Method exploits signal of genomic proximity in Hi-C datasets for ultra long range scaffolding of de novo genome assemblies. | Chromosome, scale, scaffolding, de novo, genome, assembly, chromatin, Hi-C, data, clustering, contig | NHGRI HG006283; National Science Foundation ; NHGRI T32 HG000035 |
PMID:24185095 | Free, Available for download, Freely available | SCR_017644 | Ligating Adjacent Chromatin Enables Scaffolding In Situ | 2026-02-15 09:22:06 | 62 | ||||||||
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Purge_haplotigs Resource Report Resource Website 10+ mentions |
Purge_haplotigs (RRID:SCR_017616) | software application, data processing software, software resource | Pipeline for reassigning primary contigs that should be labelled as haplotigs. Used for third generation sequencing based assemblies to automate reassignment of allelic contigs, and to assist in manual curation of genome assemblies. | Reassigning, primary, contig, label, haplotig, third, generation, sequencing, assembly, allelic, curation, genome, alignment | PMID:30497373 | Free, Available for download, Freely available | SCR_017616 | 2026-02-15 09:22:04 | 14 | ||||||||||
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Recognition of Errors in Assemblies using Paired Reads Resource Report Resource Website 1+ mentions |
Recognition of Errors in Assemblies using Paired Reads (RRID:SCR_017625) | REAPR | software application, data processing software, software resource | Software tool to identify errors in genome assemblies without need for reference sequence. Can be used in any stage of assembly pipeline to automatically break incorrect scaffolds and flag other errors in assembly for manual inspection. Reports mis-assemblies and other warnings, and produces new broken assembly based on error calls. | Identify, error, genome, assembly, without, reference, sequence, incorrect, scaffold, error |
is listed by: Debian is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
European Union ; Wellcome Trust ; JSPS KAKENHI |
PMID:23710727 | Free, Available for download, Freely available | OMICS_04068 | https://sources.debian.org/src/reapr/ | SCR_017625 | 2026-02-15 09:21:23 | 2 | |||||
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JTK_CYCLE Resource Report Resource Website 1+ mentions |
JTK_CYCLE (RRID:SCR_017962) | software application, data processing software, software resource | Software R package for Detecting Rhythmic Components in Genome-Scale Data Sets. Non-parametric algorithm to identify rhythmic components in large datasets. Identifies and characterizes cycling variables in large datasets. | Washington University in St.Louis, detecting rhythmic, component, genome, scale, dataset, algorithm, non parametric, cycling, variable | NIMH P50 MH074924; NHBLI R01 HL097800; Pennsylvania Commonwealth Health Research Formula Funds |
PMID:20876817 | Free, Freely available | SCR_017962 | Jonckheere-Terpstra-Kendall-CYCLE | 2026-02-15 09:22:18 | 5 | ||||||||
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GeSeq Resource Report Resource Website 100+ mentions |
GeSeq (RRID:SCR_017336) | software application, service resource, data processing software, software resource | Software tool for rapid and accurate annotation of organelle genomes, in particular chloroplast genomes. | rapid, accurate, annotation, organelle, genome, chloroplast, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Human Frontier Science Program ; Max Planck Society ; German Science Foundation |
PMID:28486635 | Free, Freely available | biotools:geseq | https://bio.tools/geseq | SCR_017336 | 2026-02-15 09:22:03 | 375 | ||||||
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seq-annot Resource Report Resource Website 1+ mentions |
seq-annot (RRID:SCR_018731) | software application, standalone software, software toolkit, software resource | Software Python package for annotating and counting genomic features in genomes and metagenomes. Software tools to facilitate annotation and comparison of genomes and metagenomes. | Annotating, counting, comparison, genomic feature, genome, metagenome, metagenomics, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:seq-annot | https://bio.tools/seq-annot | SCR_018731 | 2026-02-15 09:22:17 | 1 | ||||||||
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GeneSyntenyPipeline Resource Report Resource Website |
GeneSyntenyPipeline (RRID:SCR_018198) | software application, data processing software, software resource | Software pipeline was designed to draw gene synteny plot between genomes and obtain 1 to 1 gene pairs from each genome. | Genome, synteny, plot, JCVI, gene pair, data | Free, Available for download, Freely available | SCR_018198 | 2026-02-15 09:21:33 | 0 | |||||||||||
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CustomCDF Resource Report Resource Website 1+ mentions |
CustomCDF (RRID:SCR_018527) | software application, data processing software, software resource | Brainarray custom CDFs for processing raw Affymetrix data. Used to map probe to probesets. Oligonucleotide probes on GeneChips are reorganized based on latest genome and transcriptome information. | Brainarray, custom CDF, processing raw Affymetrix data, data processing, map probe, probset, oligonucleotide probe, GeneChips, genome, transcriptome, data | PMID:16284200 | Free, Freely available | https://gist.github.com/rmflight/3108891 https://rdrr.io/github/jakejh/metapredict/man/installCustomCdfPackages.html |
SCR_018527 | 2026-02-15 09:22:22 | 8 | |||||||||
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variation graph Resource Report Resource Website |
variation graph (RRID:SCR_024369) | vg | software toolkit, software resource | Software toolkit to improve read mapping by representing genetic variation in reference.Provides succinct encoding of sequences of many genomes. | read mapping, representing genetic variation in reference, encoding of sequences, genome | is listed by: Debian | PMID:30125266 | Free, Available for download, Freely available, | https://sources.debian.org/src/vg/ | SCR_024369 | variationgraph | 2026-02-15 09:22:41 | 0 | ||||||
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Four-dimensional Ascidian Body Atlas Resource Report Resource Website 1+ mentions |
Four-dimensional Ascidian Body Atlas (RRID:SCR_001691) | FABA | atlas, data or information resource, d spatial image | Image resource including ascidian's three-dimensional (3D) and cross-sectional images through the developmental time course. These images were reconstructed from more than 3,000 high-resolution real images collected by confocal laser scanning microscopy (CLSM) at newly defined 26 distinct developmental stages (stages 1-26) from fertilized egg to hatching larva, which were grouped into six periods named the zygote, cleavage, gastrula, neurula, tailbud, and larva periods. The data set will be helpful in standardizing developmental stages for morphology comparison as well as for providing guidelines for several functional studies of a body plan in chordate. | gene expression, genome, comparative genomics, human, microarray data, model organism, vertebrate, development, ascidian, embryonic development, embryo, video, developmental stage, 3d, slice, timelapse, egg, larva, time, confocal laser scanning microscopy | Japanese Ministry of Education Culture Sports Science and Technology MEXT ; JST-BIRD ; Japan Society for the Promotion of Science 18770207 |
PMID:17557317 | Free, Freely Available | nif-0000-02529 | http://ciona.lab.nig.ac.jp/ascidian/top.html | SCR_001691 | FABA: Four-dimensional Ascidian Body Atlas | 2026-02-15 09:18:09 | 5 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant 2U24DK097771-09.
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