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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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TransDecoder Resource Report Resource Website 1000+ mentions |
TransDecoder (RRID:SCR_017647) | data processing software, software application, software resource, standalone software | 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 | 2026-09-05 06:30:54 | 1572 | |||||||
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LACHESIS Resource Report Resource Website 50+ mentions |
LACHESIS (RRID:SCR_017644) | data processing software, software application, 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 | National Science Foundation ; NHGRI HG006283; NHGRI T32 HG000035 |
PMID:24185095 | Free, Available for download, Freely available | SCR_017644 | Ligating Adjacent Chromatin Enables Scaffolding In Situ | 2026-09-05 06:30:54 | 70 | ||||||||
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Purge_haplotigs Resource Report Resource Website 10+ mentions |
Purge_haplotigs (RRID:SCR_017616) | data processing software, software application, 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 | 2026-09-05 06:30:54 | 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 | data processing software, software application, 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 ; JSPS KAKENHI ; Wellcome Trust |
PMID:23710727 | Free, Available for download, Freely available | OMICS_04068 | https://sources.debian.org/src/reapr/ | SCR_017625 | 2026-09-05 06:30:54 | 2 | |||||
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JTK_CYCLE Resource Report Resource Website 1+ mentions |
JTK_CYCLE (RRID:SCR_017962) | data processing software, software application, 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 | NHBLI R01 HL097800; NIMH P50 MH074924; Pennsylvania Commonwealth Health Research Formula Funds |
PMID:20876817 | Free, Freely available | SCR_017962 | Jonckheere-Terpstra-Kendall-CYCLE | 2026-09-05 06:30:54 | 5 | ||||||||
|
GeneSyntenyPipeline Resource Report Resource Website |
GeneSyntenyPipeline (RRID:SCR_018198) | data processing software, software application, 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 | 2026-09-05 06:30:55 | 0 | |||||||||||
|
CustomCDF Resource Report Resource Website 1+ mentions |
CustomCDF (RRID:SCR_018527) | data processing software, software application, 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 | 2026-09-05 06:30:55 | 8 | |||||||||
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GenVision Resource Report Resource Website 1+ mentions |
GenVision (RRID:SCR_001166) | GenVision | commercial organization, software resource | A genomic visualization application to support easy generation of publication quality graphics and maps. It produces high quality images of annotated genomes but it can also be customized to accentuate specific areas of interest, such as comparing gene functionality, illustrating gene expression levels, and visualizing the coverage in an assembled contig. | genome, image, visualization, graphic, map, gene expression, contig, genetics |
is listed by: OMICtools works with: Lasergene's SeqMan Pro |
Commercial | OMICS_02135 | SCR_001166 | GenVision - Software for Publication-Quality Illustrations, DNASTAR GenVision | 2026-09-05 06:33:20 | 1 | |||||||
|
EBI Genomes Resource Report Resource Website 10+ mentions |
EBI Genomes (RRID:SCR_002426) | data or information resource, data set | The EBI genomes pages give access to a large number of complete genomes including bacteria, archaea, viruses, phages, plasmids, viroids and eukaryotes. Methods using whole genome shotgun data are used to gain a large amount of genome coverage for an organism. WGS data for a growing number of organisms are being submitted to DDBJ/EMBL/GenBank. Genome entries have been listed in their appropriate category which may be browsed using the website navigation tool bar on the left. While organelles are all listed in a separate category, any from Eukaryota with chromosome entries are also listed in the Eukaryota page. Within each page, entries are grouped and sorted at the species level with links to the taxonomy page for that species separating each group. Within each species, entries whose source organism has been categorized further are grouped and numbered accordingly. Links are made to: * taxonomy * complete EMBL flatfile * CON files * lists of CON segments * Project * Proteomes pages * FASTA file of Proteins * list of Proteins | eukaryote genome, gene, gene browser, genome, archaea genome, bacteria genome, phage genome, plasmid genome, viroid genome, viruse genome, sequence, protein, nucleotide, complete genome, gold standard | has parent organization: European Bioinformatics Institute | nif-0000-02778 | SCR_002426 | Genomes Pages - At the EBI, ENA Genomes Server | 2026-09-05 06:33:23 | 26 | |||||||||
|
Genomedata Resource Report Resource Website 1+ mentions |
Genomedata (RRID:SCR_004544) | Genomedata | software resource, source code | A format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. They have also developed utilities to load data into this format. Retrieving data from this format is more than 2900 times faster than a naive approach using wiggle files. A reference implementation in Python and C components is available here under the GNU General Public License. The software has only been tested on Linux and Mac systems. | genome, data, format, linux, mac, functional genomics, function, bio.tools |
is listed by: OMICtools is listed by: 3DVC is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA |
PMID:20435580 | GNU General Public License | nlx_53677, biotools:genomedata, OMICS_02148 | https://bio.tools/genomedata | SCR_004544 | 2026-09-05 06:33:25 | 1 | ||||||
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Fungal Genome Initiative Resource Report Resource Website 10+ mentions |
Fungal Genome Initiative (RRID:SCR_003169) | FGI | data or information resource, data set | Produces and analyzes sequence data from fungal organisms that are important to medicine, agriculture and industry. The FGI is a partnership between the Broad Institute and the wider fungal research community, with the selection of target genomes governed by a steering committee of fungal scientists. Organisms are selected for sequencing as part of a cohesive strategy that considers the value of data from each organism, given their role in basic research, health, agriculture and industry, as well as their value in comparative genomics. | sequence, fungi, gene annotation, genome |
is listed by: 3DVC has parent organization: Broad Institute |
NHGRI ; NSF ; NIAID ; USDA |
Free, Freely available | nif-0000-30591 | SCR_003169 | 2026-09-05 06:33:23 | 18 | |||||||
|
University of Delaware Skate Genome Project Resource Report Resource Website 1+ mentions |
University of Delaware Skate Genome Project (RRID:SCR_005300) | Skate Genome Project | access service resource, core facility, service resource | Core facility provides a model for collaborative approaches to use specialized resources and expertise in an integrated process. Core builds on the expertise and resources provided by the Bioinformatics Cores of the five northeastern states that form NECC. The Skate Genome Annotation Workshops and Jamborees offer training and opportunities for faculty and students to work with and annotate genome sequences. Workshops include lectures, tutorials and exercises annotating the genome of the little skate, Leucoraja erinacea. | skate, genome, genomics, bioinformatics, sequencing, annotate, sequence, workshop |
has parent organization: North East Cyberinfrastructure Consortium has parent organization: University of Delaware; Delaware; USA is parent organization of: SkateBase |
Available to external user | nlx_144349 | SCR_005300 | , University of Delaware, Genome Project, Skate | 2026-09-05 06:33:26 | 1 | |||||||
|
FaST LMM Resource Report Resource Website 1+ mentions |
FaST LMM (RRID:SCR_015506) | software resource, software toolkit | FaST-LMM (Factored Spectrally Transformed Linear Mixed Models) is a set of tools for efficiently performing genome-wide association studies (GWAS), prediction, and heritability estimation on large data sets. | gwas, association study, heritability, single-snp, snp-set, genome | Free, Available for download | SCR_015506 | Factored Spectrally Transformed Linear Mixed Models, fastlmm | 2026-09-05 06:33:00 | 6 | ||||||||||
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iPiG Resource Report Resource Website |
iPiG (RRID:SCR_016164) | iPiG | software application, software resource, standalone software | Standalone software tool for the integration of peptide identifications from mass spectrometry experiments into existing genome browser visualizations. | integration, peptide, spectrum, match, genome, browser, visualization, experiment, pms, ms, bio.tools |
uses: UCSC Genome Browser is listed by: bio.tools is listed by: Debian |
Robert Koch-Institute | PMID:23226516 DOI:10.1371/journal.pone.0050246 |
Free, Available for download | biotools:ipig, OMICS_06913 | https://bio.tools/ipig, https://sources.debian.org/src/ipig/ | SCR_016164 | iPiG: Integrating Peptide Spectrum Matches Into Genome Browser Visualizations | 2026-09-05 06:33:01 | 0 | ||||
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Chromosome Scale Assembler Resource Report Resource Website 1+ mentions |
Chromosome Scale Assembler (RRID:SCR_017960) | CSA | software application, software resource | Software pipeline for high-throughput chromosome level vertebrate genome assembly. Pipeline, which after contig assembly performs post assembly improvements by ordering assembly and closing gaps, as well as splitting of low supported regions. | Assembly, chromosome, vertebrate, genome, contig, closing, gap, splitting, low, supported, region, bio.tools |
is listed by: bio.tools is listed by: Debian |
German Research foundation | Free, Available for download, Freely available | biotools:csa2.6 | https://bio.tools/CSA2.6 | SCR_017960 | Chromosome Scale Assembler | 2026-09-05 06:33:03 | 5 | |||||
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ProtHint Resource Report Resource Website 50+ mentions |
ProtHint (RRID:SCR_021167) | software resource, software toolkit | Software pipeline for predicting and scoring hints (in form of introns, start and stop codons) in genome of interest by mapping and spliced aligning predicted genes to database of reference protein sequences. | Predicting and scoring hints, form of introns, start and stop codons, genome, mapping, spliced aligning, predicted genes, database, reference protein sequences | has parent organization: Georgia Institute of Technology; Georgia; USA | Free, Available for download, Freely available | SCR_021167 | 2026-09-05 06:33:07 | 51 | ||||||||||
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1000 Genomes Project and AWS Resource Report Resource Website 5000+ mentions |
1000 Genomes Project and AWS (RRID:SCR_008801) | 1000 Genomes Project and AWS | data or information resource, data set | A dataset containing the full genomic sequence of 1,700 individuals, freely available for research use. The 1000 Genomes Project is an international research effort coordinated by a consortium of 75 companies and organizations to establish the most detailed catalogue of human genetic variation. The project has grown to 200 terabytes of genomic data including DNA sequenced from more than 1,700 individuals that researchers can now access on AWS for use in disease research free of charge. The dataset containing the full genomic sequence of 1,700 individuals is now available to all via Amazon S3. The data can be found at: http://s3.amazonaws.com/1000genomes The 1000 Genomes Project aims to include the genomes of more than 2,662 individuals from 26 populations around the world, and the NIH will continue to add the remaining genome samples to the data collection this year. Public Data Sets on AWS provide a centralized repository of public data hosted on Amazon Simple Storage Service (Amazon S3). The data can be seamlessly accessed from AWS services such Amazon Elastic Compute Cloud (Amazon EC2) and Amazon Elastic MapReduce (Amazon EMR), which provide organizations with the highly scalable compute resources needed to take advantage of these large data collections. AWS is storing the public data sets at no charge to the community. Researchers pay only for the additional AWS resources they need for further processing or analysis of the data. All 200 TB of the latest 1000 Genomes Project data is available in a publicly available Amazon S3 bucket. You can access the data via simple HTTP requests, or take advantage of the AWS SDKs in languages such as Ruby, Java, Python, .NET and PHP. Researchers can use the Amazon EC2 utility computing service to dive into this data without the usual capital investment required to work with data at this scale. AWS also provides a number of orchestration and automation services to help teams make their research available to others to remix and reuse. Making the data available via a bucket in Amazon S3 also means that customers can crunch the information using Hadoop via Amazon Elastic MapReduce, and take advantage of the growing collection of tools for running bioinformatics job flows, such as CloudBurst and Crossbow. | genomic data, genome, cloud computing, cloud, human, gene, genetic variation, research, dna |
is used by: HmtVar is related to: Broad Institute Genomics Platform has parent organization: Amazon Web Services |
nlx_144340 | SCR_008801 | 1000 Genomes Project and Amazon Web Services, 000 Genomes Project Amazon Web Services, 1000 Genomes Project AWS | 2026-09-05 06:33:29 | 7076 | ||||||||
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Fungi Sequencing Projects Resource Report Resource Website 1+ mentions |
Fungi Sequencing Projects (RRID:SCR_008524) | data or information resource, data set | Fungal genomes available from the Sanger Institute. Data are accessible in a number of ways; for each organism there is a BLAST server, allowing search of the sequences. Sequences can also be down-loaded directly by FTP. In addition, for those organisms being sequenced using a cosmid approach, finished and annotated cosmids are submitted to EMBL and other public databases. | genome, genomics, sequence, fungus, blast, data analysis service | has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom | nif-0000-30593 | SCR_008524 | Fungi Sequencing | 2026-09-05 06:33:29 | 6 | |||||||||
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Montana State University Bioinformatics Core Facility Resource Report Resource Website |
Montana State University Bioinformatics Core Facility (RRID:SCR_009937) | access service resource, core facility, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core for Microarray analysis, Database development, Systems biology analysis, Genome assembly, Pathway data analysis, Expression data analysis, Metagenomics analysis. To maintain equipment and software for bioinformatic research, promote bioinformatics education on the MSU campus, and provide training and support to biologists implementing bioinformatics tools in their research. | nucleic, acid, microarray, assay, database, development, analysis, genome, assembly, pathway, data, gene, expression, metagenomics |
is listed by: Eagle I has parent organization: Montana State University |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156405 | http://cores.montana.edu/bioinformatics/ | SCR_009937 | , Montana State University, core facility, MSU, Bioinformatics Core Laboratory | 2026-09-05 06:33:37 | 0 | |||||||
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Scripps Wellderly Genome Reference Resource Report Resource Website |
Scripps Wellderly Genome Reference (RRID:SCR_010250) | SWGR | data or information resource, data set | Whole genome sequencing data for 454 unrelated Scripps Wellderly Study participants with European ancestry from a project that is studying the genetic architecture of exceptional healthspan from a cohort comprised of more than 1300 healthy individuals over the age of 80 years. SWGR_v1.0 includes chromosome-specific VCF4.1 bgzipped and tabix indexed files. Annotations for each variant can be found at Scripps Genome ADVISER (SG-ADVISER, http://genomics.scripps.edu/) Additional data releases are expected. | genomics, genomic sequence, genome, female, male, late adult human | has parent organization: Scripps Translational Science Institute | Healthy aging, Aging, Healthy | Scripps Health; California; USA ; NCATS ScienceUL1 TR00114 |
Free, Public, Acknowledgement required | nlx_156888 | SCR_010250 | 2026-09-05 06:33:43 | 0 |
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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 U24DK097771.
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