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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Wellcome Trust Sanger Institute; Hinxton; United Kingdom Resource Report Resource Website 500+ mentions |
Wellcome Trust Sanger Institute; Hinxton; United Kingdom (RRID:SCR_011784) | WTSI, Sanger | institution | Non profit research organization for genome sequences to advance understanding of biology of humans and pathogens in order to improve human health globally. Provides data which can be translated for diagnostics, treatments or therapies including over 100 finished genomes, which can be downloaded. Data are publicly available on limited basis, and provided more extensively upon request. | research, genome, sequence, human, health, project, global, data, treatment, therapy |
is listed by: re3data.org is affiliated with: Open Targets is related to: Clonalframe is related to: ClonalOrigin is related to: TraCeR is parent organization of: ILLUMINUS is parent organization of: ARNIE is parent organization of: Sequence Search and Alignment by Hashing Algorithm is parent organization of: Sequencing of Idd regions in the NOD mouse genome is parent organization of: CAROL is parent organization of: DINDEL is parent organization of: Wellcome Trust Case Control Consortium is parent organization of: OLORIN is parent organization of: Exomiser is parent organization of: COSMIC - Catalogue Of Somatic Mutations In Cancer is parent organization of: GeneDB is parent organization of: Breast Cancer Somatic Genetics Study is parent organization of: Artemis: Genome Browser and Annotation Tool is parent organization of: ACT: Artemis Comparison Tool is parent organization of: Alien hunter is parent organization of: Pfam is parent organization of: DNAPlotter is parent organization of: VAGrENT is parent organization of: SMALT is parent organization of: LookSeq is parent organization of: ZMP is parent organization of: Deciphering Developmental Disorders is parent organization of: Sanger Mouse Resources Portal is parent organization of: SpliceDB is parent organization of: DECIPHER is parent organization of: 1000 Genomes: A Deep Catalog of Human Genetic Variation is parent organization of: Genes to Cognition: Neuroscience Research Programme is parent organization of: MEROPS is parent organization of: Rfam is parent organization of: VEGA is parent organization of: Bacterial Genomes is parent organization of: Caenorhabditis Genome Sequencing Projects is parent organization of: D. rerio Blast Server is parent organization of: Fungi Sequencing Projects is parent organization of: PEER is parent organization of: Alfresco - FRont-End for Sequence COmparison is parent organization of: AutoCSA (Automatic Comparative Sequence Analysis) is parent organization of: AceDB is parent organization of: CnD is parent organization of: Genomics of Drug Sensitivity in Cancer is parent organization of: Zebrafish Genome Project is parent organization of: Tree families database is parent organization of: Ensembl is parent organization of: BamView is parent organization of: SVMerge is parent organization of: RetroSeq is parent organization of: Consensus CDS is parent organization of: WormBase is parent organization of: Belvu is parent organization of: Bio-tradis is parent organization of: Blixem is parent organization of: Dotter is parent organization of: Exonerate is parent organization of: Fastaq is parent organization of: Gubbins is parent organization of: CellPhoneDB is parent organization of: Ensembl Metazoa is parent organization of: Scmap is parent organization of: Scfind is parent organization of: Recognition of Errors in Assemblies using Paired Reads is parent organization of: SAMTOOLS is parent organization of: Cell Model Passports |
Wellcome Trust | ISNI: 0000 0004 0606 5382, nlx_91258, grid.10306.34, Wikidata: Q1142544 | https://ror.org/05cy4wa09 | SCR_011784 | Wellcome Trust Sanger Institute, Genome Research Limited, The Wellcome Sanger Institute, Sanger Institute, Wellcome Trust Sanger Institute Genome Research Limited | 2026-08-01 12:04:18 | 527 | ||||||
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ClonalOrigin Resource Report Resource Website 1+ mentions |
ClonalOrigin (RRID:SCR_016061) | data processing software, data analysis software, software resource, sequence analysis software, software application | Software package for comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry. | comparative, analysis, sequence, bacteria, genome, reconstruct, recombination, events, ancestry, bayesian |
is listed by: Debian is listed by: OMICtools is related to: Imperial College London; London; United Kingdom is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust WT082930MA; National Science Foundation DBI-0630765; Science Foundation of Ireland 05/FE1/B882 |
PMID:20923983 DOI:10.1534/genetics.110.120121 |
Free, Available for download | OMICS_18881 | https://sources.debian.org/src/clonalorigin/ | SCR_016061 | 2026-08-04 09:43:48 | 8 | ||||||
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Clonalframe Resource Report Resource Website 100+ mentions |
Clonalframe (RRID:SCR_016060) | data processing software, data analysis software, software resource, sequence analysis software, software application | Software package for the inference of bacterial microevolution using multilocus sequence data. It is used to identify the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance. | analysis, sequence, inference, bacteria, microevolution, multilocus, clonal, sample, chromosome, homologuous, recombination, disrupted, inheritance, DNA, genome |
is listed by: Debian is listed by: OMICtools is related to: Imperial College London; London; United Kingdom is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust | DOI:10.1534/genetics.106.063305 | Free, Available for download | OMICS_14623 | https://github.com/xavierdidelot/ClonalFrameML, https://sources.debian.org/src/clonalframe/ | SCR_016060 | ClonalFrameML | 2026-08-04 09:43:47 | 379 | |||||
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TraCeR Resource Report Resource Website 10+ mentions |
TraCeR (RRID:SCR_016338) | simulation software, data processing software, data analysis software, software resource, software application, software toolkit | Software application for recovery of T cell receptor (TCR) data from single cell data. Used to reconstruct full-length, paired T cell receptor (TCR) sequences from T lymphocyte single-cell RNA sequence data. Links T cell specificity with functional response by revealing clonal relationships between cells alongside their transcriptional profiles. | recovery, receptor, single, cell, data, computation, method, reconstruct, sequence, T lymphocyte, RNA, sequence |
is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is related to: European Bioinformatics Institute |
European Research Council ; the Lister Institute for Preventative Medicine (S.A.T.) |
PMID:26950746 | Free, Available for download, Freely available | SCR_016338 | 2026-08-04 09:43:52 | 13 | ||||||||
|
CnD Resource Report Resource Website |
CnD (RRID:SCR_010818) | CnD | software resource | A program to detect copy number variants from short read sequence data. |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
OMICS_00338 | SCR_010818 | 2026-08-01 12:03:58 | 0 | ||||||||||
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SVMerge Resource Report Resource Website 10+ mentions |
SVMerge (RRID:SCR_004777) | SVMerge | software resource | Software pipeline to detect structural variants (SVs) by integrating calls from several existing SV callers, which are then validated and the breakpoints refined using local de novo assembly. The output is in BED format allowing for easy downstream analysis or viewing in a genome browser. It is modular and extensible allowing new callers to be incorporated as they become available. | structural variant, breakpoint, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:21194472 | biotools:svmerge, OMICS_00325 | https://bio.tools/svmerge | SCR_004777 | SVMerge - Enhanced structural variant and breakpoint detection | 2026-08-01 12:02:40 | 19 | ||||||
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LookSeq Resource Report Resource Website 1+ mentions |
LookSeq (RRID:SCR_005625) | LookSeq | software resource | A web-based application for alignment visualization, browsing and analysis of genome sequence data. | alignment, visualization, browsing, analysis, genome, sequence |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
OMICS_00886 | SCR_005625 | 2026-08-01 12:03:00 | 5 | |||||||||
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Artemis: Genome Browser and Annotation Tool Resource Report Resource Website 100+ mentions |
Artemis: Genome Browser and Annotation Tool (RRID:SCR_004267) | Artemis | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Free genome browser and annotation tool that allows visualization of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. Artemis is free software and is distributed under the terms of the GNU General Public License. Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format. | training tool, genome browser, gene annotation, java, bio.tools |
is listed by: OMICtools is listed by: 3DVC is listed by: Debian is listed by: bio.tools is related to: DNAPlotter has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom works with: Alien-hunter |
Wellcome Trust | PMID:11120685 DOI:10.1093/bioinformatics/btr703 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_28554, OMICS_00903, biotools:artemis | https://bio.tools/artemis, https://sources.debian.org/src/art-nextgen-simulation-tools/ | SCR_004267 | 2026-08-01 12:02:34 | 421 | |||||
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VAGrENT Resource Report Resource Website 10+ mentions |
VAGrENT (RRID:SCR_005180) | VAGrENT | software toolkit, software resource | Software tool set for calculating the biological consequences of genomic variations. The suite of perl modules compares genomic variations with reference genome annotations and generates the possible effects each variant may have on the transcripts it overlaps. It evaluates each variation/transcript combination and describes the effects in the mRNA, CDS and protein sequence contexts. It provides details of the sequence and position of the change within the transcript / protein as well as Sequence Ontology terms to classify its consequences. | perl, genomic variation, transcript, mrna, cds, protein sequence, protein, sequence |
is listed by: OMICtools is related to: SO has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
OMICS_00192 | SCR_005180 | VAGrENT: Variation Annotation Generator, Variation Annotation Generator | 2026-08-02 09:04:09 | 14 | ||||||||
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Blixem Resource Report Resource Website 1+ mentions |
Blixem (RRID:SCR_015994) | data processing software, alignment software, software resource, software application, image analysis software | Software for sequence alignments that displays multiple match sequences aligned against a single genomic reference sequence. It can be used for manipulation, display and annotation of genomic data, to check the quality of an alignment, to find missing/misaligned sequence, and to identify splice sites and polyA sites. | software, sequence, alignment, annotation, genomic, reference, data, display, manipulation, DNA |
is related to: SEQtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust Grant 098051; NHGRI U54 HG00455 |
PMID:26801397 | Free, Available for download | SCR_015994 | SEQtools Blixem | 2026-08-04 09:43:47 | 2 | |||||||
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1000 Genomes: A Deep Catalog of Human Genetic Variation Resource Report Resource Website 5000+ mentions |
1000 Genomes: A Deep Catalog of Human Genetic Variation (RRID:SCR_006828) | 1000 Genomes | portal, data set, consortium, organization portal, database, data or information resource | International collaboration producing an extensive public catalog of human genetic variation, including SNPs and structural variants, and their haplotype contexts, in an effort to provide a foundation for investigating the relationship between genotype and phenotype. The genomes of about 2500 unidentified people from about 25 populations around the world were sequenced using next-generation sequencing technologies. Redundant sequencing on various platforms and by different groups of scientists of the same samples can be compared. The results of the study are freely and publicly accessible to researchers worldwide. The consortium identified the following populations whose DNA will be sequenced: Yoruba in Ibadan, Nigeria; Japanese in Tokyo; Chinese in Beijing; Utah residents with ancestry from northern and western Europe; Luhya in Webuye, Kenya; Maasai in Kinyawa, Kenya; Toscani in Italy; Gujarati Indians in Houston; Chinese in metropolitan Denver; people of Mexican ancestry in Los Angeles; and people of African ancestry in the southwestern United States. The goal Project is to find most genetic variants that have frequencies of at least 1% in the populations studied. Sequencing is still too expensive to deeply sequence the many samples being studied for this project. However, any particular region of the genome generally contains a limited number of haplotypes. Data can be combined across many samples to allow efficient detection of most of the variants in a region. The Project currently plans to sequence each sample to about 4X coverage; at this depth sequencing cannot provide the complete genotype of each sample, but should allow the detection of most variants with frequencies as low as 1%. Combining the data from 2500 samples should allow highly accurate estimation (imputation) of the variants and genotypes for each sample that were not seen directly by the light sequencing. All samples from the 1000 genomes are available as lymphoblastoid cell lines (LCLs) and LCL derived DNA from the Coriell Cell Repository as part of the NHGRI Catalog. The sequence and alignment data generated by the 1000genomes project is made available as quickly as possible via their mirrored ftp sites. ftp://ftp.1000genomes.ebi.ac.uk ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes | genetic variation, gene, next-generation sequencing, sequence, alignment, genome, single-nucleotide polymorphism, structural variant, haplotype, genome-wide association study, pharmacology, genetics, biomarker, consortium, data sharing, genotype, phenotype, FASEB list |
uses: NHGRI Sample Repository for Human Genetic Research is used by: BioSample Database at EBI is listed by: OMICtools is listed by: re3data.org is listed by: Consortia-pedia is related to: MOSAIK is related to: ART is related to: SNAP - SNP Annotation and Proxy Search has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom has parent organization: Harvard Medical School; Massachusetts; USA has parent organization: Broad Institute has parent organization: NCBI has parent organization: European Bioinformatics Institute has parent organization: National Human Genome Research Institute |
Wellcome Trust Sanger Institute; Hinxton; United Kingdom ; Beijing Genomics Institute; Shenzhen; China ; NHGRI ; 454 Life Sciences Roche ; Life Technologies ; Illumina |
Free, Public, Restrictions apply, Http://www.1000genomes.org/data#DataAccess | r3d100010180, nlx_143819, OMICS_00261 | https://doi.org/10.17616/R3CP4M | SCR_006828 | International 1000 Genomes Project, 1000 Genomes Project | 2026-08-04 09:41:42 | 5486 | |||||
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Scfind Resource Report Resource Website 1+ mentions |
Scfind (RRID:SCR_017339) | data processing software, software application, software resource, data or information resource | Software R package as search tool for single cell RNA-seq data by gene lists. Builds index from scRNA-seq datasets which organizes information in suitable and compact manner so that datasets can be very efficiently searched for either cells or cell types in which given list of genes is expressed. | Single, cell, RNA-seq, data, gene, list, build, index, organize |
is listed by: Bioconductor has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Free, Available for download, Freely available | https://genat.uk/post/scfind/, http://bioconductor.org/packages/scfind/, https://github.com/hemberg-lab/scfind | SCR_017339 | 2026-08-04 09:44:09 | 1 | |||||||||
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WormBase Resource Report Resource Website 1000+ mentions |
WormBase (RRID:SCR_003098) | WB, WB REF, WP | storage service resource, data repository, service resource, database, data or information resource | Central data repository for nematode biology including complete genomic sequence, gene predictions and orthology assignments from range of related nematodes.Data concerning genetics, genomics and biology of C. elegans and related nematodes. Derived from initial ACeDB database of C. elegans genetic and sequence information, WormBase includes genomic, anatomical and functional information of C. elegans, other Caenorhabditis species and other nematodes. Maintains public FTP site where researchers can find many commonly requested files and datasets, WormBase software and prepackaged databases. | RIN, Resource Information Network, catalog, database, blast, genomic sequence, gene prediction, orthology assignment, gene function, ortholog, roundworm, geneotype, phenotype, gene mapping, genomics, gene expression, transposon family, c elegans, wormmart, FASEB list, RRID Community Authority |
uses: InterMOD is used by: NIF Data Federation is used by: Resource Identification Portal is used by: PhenoGO is used by: Integrated Animals is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: re3data.org is listed by: InterMOD is listed by: Resource Information Network is affiliated with: InterMOD is related to: AmiGO is related to: GBrowse is related to: Textpresso is related to: Expression Patterns for C. elegans promoter GFP fusions is related to: C. elegans Gene Knockout Consortium is related to: NIH Data Sharing Repositories is related to: UniParc at the EBI is related to: UniParc is related to: Integrated Manually Extracted Annotation is related to: PhenoGO has parent organization: Cold Spring Harbor Laboratory has parent organization: Washington University in St. Louis; Missouri; USA has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is parent organization of: C. elegans Development Vocabulary is parent organization of: C. elegans Gross Anatomy Vocabulary is parent organization of: C. elegans Phenotype Vocabulary is parent organization of: OpenWorm works with: A plasmid Editor is organization facet of: Alliance of Genome Resources |
NHGRI ; NIH Blueprint for Neuroscience Research ; MRC ; BBSRC ; NHGRI U41 HG002223; NIHGRI P41 HG02223 |
PMID:24194605 PMID:19910365 PMID:17991679 PMID:15608221 |
nif-0000-00053, OMICS_01664, r3d100010424 | http://www.wormbase.org/#01-23-6, https://doi.org/10.17616/R3089Z | SCR_003098 | , WB, Worm Base, WB REF, WP | 2026-08-04 09:40:49 | 1825 | |||||
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Ensembl Resource Report Resource Website 10000+ mentions |
Ensembl (RRID:SCR_002344) | database, data or information resource | Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species. | collection, genome, dataset, database, vertebrate, eukaryotic, DNA, protein, sequence, search, automaticly, annotate, data, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: Animal QTLdb is used by: ChannelPedia is used by: Blueprint Epigenome is used by: HmtPhenome lists: Ensembl Covid-19 is listed by: OMICtools is listed by: Biositemaps is listed by: re3data.org is listed by: LabWorm is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Ensembl Genomes is related to: GermOnline is related to: CandiSNPer is related to: Human Splicing Finder is related to: NGS-SNP is related to: Sanger Mouse Resources Portal is related to: DECIPHER is related to: Ensembl Genomes is related to: PeptideAtlas is related to: AnimalTFDB is related to: Bgee: dataBase for Gene Expression Evolution is related to: FlyMine is related to: Rat Gene Symbol Tracker is related to: UniParc at the EBI is related to: go-db-perl is related to: UniParc is related to: g:Profiler is related to: RIKEN integrated database of mammals is related to: VBASE2 is related to: p300db is related to: ShinyGO has parent organization: European Bioinformatics Institute has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is parent organization of: Ensembl Metazoa is parent organization of: Ensembl Variation is parent organization of: Pre Ensembl is parent organization of: Variant Effect Predictor is parent organization of: Ensembl Bacteria is parent organization of: Ensembl Plants is parent organization of: Ensembl Fungi is parent organization of: Ensembl Protists is parent organization of: Ensembl Genome Browser works with: Genotate works with: CellPhoneDB works with: Open Regulatory Annotation Database works with: Database of genes related to Repeat Expansion Diseases works with: TarBase |
Wellcome Trust ; EMBL ; European Union ; FP7 ; FP6 ; MRC ; NHGRI ; BBSRC |
PMID:24316576 PMID:23203987 |
nif-0000-21145, OMICS_01647, biotools:ensembl, r3d100010228 | https://bio.tools/ensembl, https://sources.debian.org/src/ensembl/, https://doi.org/10.17616/R39K5B | SCR_002344 | ENSEMBL | 2026-08-04 09:40:38 | 11652 | ||||||
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Sequencing of Idd regions in the NOD mouse genome Resource Report Resource Website 1+ mentions |
Sequencing of Idd regions in the NOD mouse genome (RRID:SCR_001483) | Sequencing of Idd regions in the NOD mouse genome | resource, data set, data or information resource | Genetic variations associated with type 1 diabetes identified by sequencing regions of the non-obese diabetic (NOD) mouse genome and comparing them with the same areas of a diabetes-resistant C57BL/6J reference mouse allowing identification of single nucleotide polymorphisms (SNPs) or other genomic variations putatively associated with diabetes in mice. Finished clones from the targeted insulin-dependent diabetes (Idd) candidate regions are displayed in the NOD clone sequence section of the website, where they can be downloaded either as individual clone sequences or larger contigs that make up the accession golden path (AGP). All sequences are publicly available via the International Nucleotide Sequence Database Collaboration. Two NOD mouse BAC libraries were constructed and the BAC ends sequenced. Clones from the DIL NOD BAC library constructed by RIKEN Genomic Sciences Centre (Japan) in conjunction with the Diabetes and Inflammation Laboratory (DIL) (University of Cambridge) from the NOD/MrkTac mouse strain are designated DIL. Clones from the CHORI-29 NOD BAC library constructed by Pieter de Jong (Children's Hospital, Oakland, California, USA) from the NOD/ShiLtJ mouse strain are designated CHORI-29. All NOD mouse BAC end-sequences have been submitted to the International Nucleotide Sequence Database Consortium (INSDC), deposited in the NCBI trace archive. They have generated a clone map from these two libraries by mapping the BAC end-sequences to the latest assembly of the C57BL/6J mouse reference genome sequence. These BAC end-sequence alignments can then be visualized in the Ensembl mouse genome browser where the alignments of both NOD BAC libraries can be accessed through the Distributed Annotation System (DAS). The Mouse Genomes Project has used the Illumina platform to sequence the entire NOD/ShiLtJ genome and this should help to position unaligned BAC end-sequences to novel non-reference regions of the NOD genome. Further information about the BAC end-sequences, such as their alignment, variation data and Ensembl gene coverage, can be obtained from the NOD mouse ftp site. | genome, sequencing, genome sequencing, insulin-dependent diabetes, c57bl/6j, single nucleotide polymorphism, genetic variation, bacterial artificial chromosome, sequence, gene, animal model, clone, annotation, contig |
lists: VEGA is listed by: NIDDK Information Network (dkNET) has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Type 1 diabetes, Diabetes | NIAID AI 15416; NIDDK ; JDRF |
PMID:23729657 | Free, Freely available | nlx_152738 | http://www.sanger.ac.uk/resources/mouse/nod/ | SCR_001483 | Sequencing of Insulin-dependent diabetes regions in the NOD mouse genome | 2026-08-04 09:40:24 | 1 | |||
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Ensembl Metazoa Resource Report Resource Website 10+ mentions |
Ensembl Metazoa (RRID:SCR_000800) | database, data or information resource | Ensembl Genomes project produces genome databases for important species from across taxonomic range, using Ensembl software system. Five sites are now available, one of which is Ensembl Metazoa, which houses metazoan species. | database, genome, metazoan, software, specie, taxonomic, FASEB list |
has parent organization: Ensembl has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom has parent organization: European Bioinformatics Institute |
EMBL - EBI | PMID:21785142 | r3d100011198, nif-0000-33714 | SCR_000800 | EnsemblMetazoa | 2026-08-04 09:40:14 | 37 | |||||||
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Exomiser Resource Report Resource Website 50+ mentions |
Exomiser (RRID:SCR_002192) | Exomiser, Exomiser2 | data analysis service, analysis service resource, software resource, production service resource, service resource | A Java program that functionally annotates variants from whole-exome sequencing data starting from a VCF (Variant Call Format) file (version 4). The functional annotation code is based on Annovar and uses UCSCKnownGene transcript definitions and hg19 genomic coordinates. Variants are prioritized according to user-defined criteria on variant frequency, pathogenicity, quality, inheritance pattern, phenotype data from human and model organisms, and proximity in the interactome to phenotypically similar genes. | java, functional annotation, function, variant, whole-exome sequencing, gene, phenotype, model organism |
uses: dbNSFP has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:24162188 | Free, Freely available | SciRes_000142 | SCR_002192 | The Exomiser2: Annotate and Filter Variants, Exomiser2: Annotate and Filter Variants, Exomiser 2.0 | 2026-08-04 09:40:35 | 60 | ||||||
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DECIPHER Resource Report Resource Website 1000+ mentions |
DECIPHER (RRID:SCR_006552) | DECIPHER | database, data or information resource | Interactive database which incorporates a suite of tools designed to aid the interpretation of submicroscopic chromosomal imbalance. Used to enhance clinical diagnosis by retrieving information from bioinformatics resources relevant to the imbalance found in the patient. Contributing to the DECIPHER database is a Consortium, comprising an international community of academic departments of clinical genetics. Each center maintains control of its own patient data (which are password protected within the center''''s own DECIPHER project) until patient consent is given to allow anonymous genomic and phenotypic data to become freely viewable within Ensembl and other genome browsers. Once data are shared, consortium members are able to gain access to the patient report and contact each other to discuss patients of mutual interest, thus facilitating the delineation of new microdeletion and microduplication syndromes. | chromosomal imbalance, phenotype, chromosome, gene, genome, deletion, duplication, copy number, genotype, polymorphism, FASEB list |
is used by: MARRVEL is listed by: OMICtools is related to: Deciphering Developmental Disorders is related to: Ensembl has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Developmental disorder, Microdeletion Syndrome, Overgrowth syndrome, Microduplication syndrome, Deletion syndrome, Duplication syndrome, Wolf-Hirschhorn Syndrome, Williams-Beuren Syndrome, Smith-Magenis Syndrome, Etc | Wellcome Trust WT077008 | PMID:19344873 | Acknowledgement required | nlx_151653, OMICS_00265 | SCR_006552 | Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources, DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources, Database of Chromosomal Imbalance Phenotype in Humans using Ensembl Resources, Decipher | 2026-08-04 09:41:38 | 1797 | ||||
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ILLUMINUS Resource Report Resource Website |
ILLUMINUS (RRID:SCR_000388) | Illuminus | software application, software resource | A fast and accurate algorithm for assigning single nucleotide polymorphism (SNP) genotypes to microarray data from the Illumina BeadArray technology. | gene, genetic, genomic, c++, single nucleotide polymorphism, genotype, microarray, illumina beadarray, illumina |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:17846035 | Free, Available for download, Freely available | OMICS_00726, nlx_154408 | http://www.sanger.ac.uk/resources/software/illuminus/ | http://www.sanger.ac.uk/science/tools/illuminus | SCR_000388 | Illuminus: the genotype calling algorithm | 2026-08-04 09:40:07 | 0 | ||||
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CAROL Resource Report Resource Website 10+ mentions |
CAROL (RRID:SCR_001800) | CAROL | software application, software resource | Software application that is a combined functional annotation score of non-synonymous coding variants. A major challenge in interpreting whole-exome data is predicting which of the discovered variants are deleterious or neutral. To address this question in silico, they have developed a score called Combined Annotation scoRing toOL (CAROL), which combines information from two bioinformatics tools: PolyPhen-2 and SIFT, in order to improve the prediction of the effect of non-synonymous coding variants. The combination of annotation tools can help improve automated prediction of whole-genome/exome non-synonymous variant functional consequences. (entry from Genetic Analysis Software) The software should run on any UNIX or GNU/Linux system. | gene, genetic, genomic, r, prediction, non-synonymous coding variant |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:22261837 | Free, Available for download, Freely available | nlx_154254, OMICS_00143 | http://www.sanger.ac.uk/resources/software/carol/ | SCR_001800 | Combined Annotation scoRing toOL | 2026-08-04 09:40:28 | 11 |
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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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