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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SOAP Resource Report Resource Website 100+ mentions |
SOAP (RRID:SCR_000689) | SOAP, | data processing software, software application, software resource | Software package that provides full solution to next generation sequencing data analysis consisting of an alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder ( SOAPindel ), a structural variation scanner ( SOAPsv ), a de novo short reads assembler ( SOAPdenovo ), and a GPU-accelerated alignment tool for aligning short reads with a reference sequence. (SOAP3/GPU)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, next generation sequencing, alignment, short read, bio.tools |
lists: SOAPfusion lists: SOAPfuse lists: SOAPnuke lists: GapCloser is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: BGI; Shenzhen; China is parent organization of: SOAP3 is parent organization of: SOAPaligner/soap2 |
PMID:18227114 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154652, biotools:soap | https://bio.tools/soap | SCR_000689 | SOAP: short oligonucleotide alignment program, Short Oligonucleotide Analysis Package | 2026-09-12 01:00:51 | 403 | |||||
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TIDE BC Resource Report Resource Website 10+ mentions |
TIDE BC (RRID:SCR_003924) | TIDE | data or information resource, portal | A collaborative care and research initiative with a focus on prevention and treatment of Intellectual disability (ID) that is due to inborn errors of metabolism (IEM), which can be treated with diet or drugs. Health care policy and institutional culture is still operating under the old premise that all ID is incurable and thus, many children born with treatable ID are at risk of not being treated. To acknowledge the multidisciplinary scope and the ways in which health care professionals and researchers will collaborate, the goals of the TIDE BC project are demonstrated within a framework of 7 Work Packages: * Implementation of a new Protocol for diagnostic evaluation of ID, focusing of treatable conditions; * Development of infrastructure to facilitate implementation, evaluation and sustainability of the Protocol; * Investments into next generation genomic technologies; * Improving evidence of and access to treatments; * Evaluation and health economy; * Knowledge dissemination; * Education and Mentoring. The objectives addressed in all Work Packages reflect a highly integrated cluster combining clinical care, research, evaluation, and knowledge dissemination. | child, prevention, treatment, pediatric, genetic | Intellectual disability, Inborn error of metabolism | BC Childrens Hospital Foundation | nlx_158289 | SCR_003924 | TIDE-BC, Treatable Intellectual Disability Endeavor in B.C. | 2026-09-12 01:00:54 | 27 | |||||||
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Turkish Human Mutation Database Resource Report Resource Website |
Turkish Human Mutation Database (RRID:SCR_008246) | data or information resource, database | The Molecular Biology and Genetics Department at Bogazii University is one of the major reference laboratories in Turkey, specialized in molecular analysis of common genetic disorders. Over the years, the rapid accumulation of mutation data in connection with detailed clinical and laboratory information, has led to the idea of establishing a national database for storing, analysing and presenting it in a more efficient and systematic way. For this purpose, an interdisciplinary project was initiated in 1995. b-Thalassemia and Hemophilia-B Databases were selected as preliminary models, for they offer alternative design and implementation strategies due to different clinical and genetic characteristics. b-Thalassemia is an autosomal recessive disorder, characterized by microcytosis and hemolytic anemia, which is the result of reduced b-Globin chain synthesis. In Turkey, the disease is represented with a gene frequency of 2 and reflected by a wide spectrum of clinical manifestations with the presence of more than 40 different mutation. Currently, there is no database available for thalassemia mutations. Hemophilia B is an X-linked recessive disorder caused by heterogenous mutations, resulting in a marked deficit of coagulation factor IX (FIX); an essential component of the clotting mechanism. A hemophilia B database was first published in 1990 as a list of point mutations and short additions and deletions with 115 mutations comprising 216 entries Gene-, System-, or Disease- Specific Databases | gene-, genetic, anemia, autosomal, b-globin, biology, b-thalassemia, clinical, clotting, coagulation, disorder, hemolytic, hemophilia-b, heterogenous, laboratory, mechanism, microcytosis, model, molecular, mutation, or disease- specific databases, synthesis, system- | nif-0000-21404 | http://www.medinfo.hacettepe.edu.tr/hmuttr/ | SCR_008246 | Human Mutation Database | 2026-09-12 01:01:59 | 0 | |||||||||
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Daphnia genomics consortium Resource Report Resource Website 10+ mentions |
Daphnia genomics consortium (RRID:SCR_008148) | data or information resource, database | The Daphnia Genomics Consortium (DGC) is an international network of investigators committed to mounting the freshwater crustacean Daphnia as a model system for ecology, evolution and the environmental sciences. Along with research activities, the DGC is: (1) coordinating efforts towards developing the Daphnia genomic toolbox, which will then be available for use by the general community; (2) facilitating collaborative cross-disciplinary investigations; (3) developing bioinformatic strategies for organizing the rapidly growing genome database; and (4) exploring emerging technologies to improve high throughput analyses of molecular and ecological samples. If we are to succeed in creating a new model system for modern life-sciences research, it will need to be a community-wide effort. Research activities of the DGC are primarily focused on creating genomic tools and information. When completed, the current projects will offer a first view of the Daphnia genome''s topography, including regions of high and low recombination, the distribution of transposable, repetitive and regulatory elements, the size and structure of genes and of their neighborhoods. This information is crucial in formulating testable hypotheses relating genetics and demographics to the evolutionary potential or constraints of natural populations. Projects aiming to compile identifiable genes with their function are also underway, together with robust methods to verify these findings. Finally, these tools are being tested, by exploring their uses in key ecological and toxicological investigations. Each project benefits from the leadership and expertise of many individuals. For further details, begin by contacting the project directors. The DGC consists of biologists from a broad spectrum of subdisciplines, including limnology, ecotoxicology, quantitative and population genetics, systematics, molecular biology and evolution, developmental biology, genomics and bioinformatics. In many regards, the rapid early success of the consortium results from its grass-roots origin promoting an international composition, under a cooperative model, with significant scientific breadth. We hold to this approach in building this network and encourage more people to participate. All the while, the DGC is structured to effectively reach specific goals. The consortium includes an advisory board (composed of experts of the various subdisciplines), whose responsibility is to act as the research community''s agent in guiding the development of Daphnia genomic resources. The advisors communicate directly to DGC members, who are either contributing genomic tools or actively seeking funds for this function. The consortium''s main body (given the widespread interest in applying genomic tools in environmental studies) are the affiliates, who make use of these tools for their research and who are soliciting support. | ecological, ecology, ecotoxicology, element, environmental science, evolution, evolutionary, freshwater, gene, genetic, basic research knowledge base, bioinformatic, biology, crustacean, daphnia, demographic, developmental, genomic, limnology, model, molecular, natural, recombination, regulatory, repetitive, size, structure, system, systematic, topography, toxicological, transposable | has parent organization: Indiana University; Indiana; USA | nif-0000-20973 | http://daphnia.cgb.indiana.edu/ | SCR_008148 | DGC | 2026-09-12 01:01:58 | 21 | ||||||||
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Brain and Body Genetic Resource Exchange Resource Report Resource Website 1+ mentions |
Brain and Body Genetic Resource Exchange (RRID:SCR_008959) | BB-GRE | data or information resource, database | A database and associated tools for investigating the genetic basis of neurodisability. It combines phenotype information from patients with neurodevelopmental and behavioral problems with clinical genetic data, and displays this information on the human genome map. Basic access to genetic information (deletions, duplications) relating to participants with neurodevelopmental disorders is provided without an account; access to the full dataset requires an account. The genetic information that is available to view comprises potentially pathogenic copy number variation across the genome, detected by array comparative genome hybridization (aCGH) using a customized 44K oligonucleotide array. | developmental disorder, copy number, neurodevelopmental disorder, child, phenotype, genotype-phenotype, brain, genetic, gene, genotype, behavior, clinical, genome, neurodevelopment, behavioral disorder, genetic variant, development | has parent organization: King's College London; London; United Kingdom | Schizophrenia, Mental retardation, Attention deficit hyperactivity disorder, Developmental language delay, Dyslexia, Sleep disorder, Epilepsy, Dysmorphism, Neurodisability, Autism | Acknowledgement required | nlx_151987 | http://bbgre-dev.iop.kcl.ac.uk/info/about-us | SCR_008959 | BBGRE.org, Brain & Body Genetic Resource Exchange, BB-GRE database | 2026-09-12 01:02:02 | 1 | |||||
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Mouse Genome Database Resource Report Resource Website 500+ mentions |
Mouse Genome Database (RRID:SCR_012953) | MGD | data or information resource, database | Community model organism database for laboratory mouse and authoritative source for phenotype and functional annotations of mouse genes. MGD includes complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information, all serving to further the use of the mouse as a model system for studying human biology and disease. MGD is a major component of the Mouse Genome Informatics.Contains standardized descriptions of mouse phenotypes, associations between mouse models and human genetic diseases, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information. Data are obtained and integrated via manual curation of the biomedical literature, direct contributions from individual investigators and downloads from major informatics resource centers. MGD collaborates with the bioinformatics community on the development and use of biomedical ontologies such as the Gene Ontology (GO) and the Mammalian Phenotype (MP) Ontology. | gene, genome, genetic, chromosome, clone, cytogenetic, dna, genomic, inbred, mammalian, mouse, mutant, ortholog, phenotype, primer, protein, reagent, sequence, strain, bio.tools |
is used by: DisGeNET is listed by: Debian is listed by: bio.tools is related to: Mouse Genome Informatics (MGI) has parent organization: Jackson Laboratory |
NHGRI HG000330 | PMID:21051359 | biotools:mgi, biotools:mgd, nif-0000-10301 | http://www.informatics.jax.org/mgihome/projects/overview.shtml, https://bio.tools/mgd, https://bio.tools/mgi | SCR_012953 | Mouse Genome Informatics: Mouse Genome Database, MGID, Mouse Genome Informatics Database | 2026-09-12 01:02:09 | 545 | |||||
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Genetic Association Database Resource Report Resource Website 100+ mentions |
Genetic Association Database (RRID:SCR_013264) | data or information resource, database | The Genetic Association Database is an archive of human genetic association studies of complex diseases and disorders. The goal of this database is to allow the user to rapidly identify medically relevant polymorphism from the large volume of polymorphism and mutational data, in the context of standardized nomenclature. The data is from published scientific papers. Study data is recorded in the context of official human gene nomenclature with additional molecular reference numbers and links. It is gene centered. That is, each record is a record of a gene or marker. If a study investigated 6 genes for a particular disorder, there will be 6 records. Anyone may view this database and anyone may submit records. You do not have to be an author on the original study to submit a record. All submitted records will be reviewed before inclusion in the archive. Both genetic and environmental factors contribute to human diseases. Most common diseases are influenced by a large number of genetic and environmental factors, most of which individually have only a modest effect on the disease. Though genetic contributions are relatively well characterized for some monogenetic diseases, there has been no effort at curating the extensive list of environmental etiological factors. From a comprehensive search of the MeSH annotation of MEDLINE articles, they identified 3,342 environmental etiological factors associated with 3,159 diseases. They also identified 1,100 genes associated with 1,034 complex diseases from the NIH Genetic Association Database (GAD), a database of genetic association studies. 863 diseases have both genetic and environmental etiological factors available. Integrating genetic and environmental factors results in the etiome, which they define as the comprehensive compendium of disease etiology. | environmental, etiological, etiology, factor, gene, general human genetics databases, genetic, association, complex, disease, disorder, human, medically, molecular, monogenetic, mutational, nomenclature, polymorphism, scientific, FASEB list |
is used by: DisGeNET is related to: KOBAS has parent organization: National Institute on Aging |
Aging | nif-0000-21163 | SCR_013264 | GAD | 2026-09-12 01:02:10 | 170 | ||||||||
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LAMBDAA Resource Report Resource Website |
LAMBDAA (RRID:SCR_001128) | LAMBDAA | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154421 | SCR_001128 | 2026-09-12 01:02:25 | 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 | 2026-09-12 01:02:26 | 11 | |||||
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LDMET Resource Report Resource Website 1+ mentions |
LDMET (RRID:SCR_001127) | LDMET | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, c | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154027 | SCR_001127 | 2026-09-12 01:02:25 | 1 | ||||||||
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CASAVA Resource Report Resource Website 1000+ mentions |
CASAVA (RRID:SCR_001802) | CASAVA | software application, software resource | Software package that creates genomic builds, calls SNPs, detects indels, and counts reads from data generated from one or more sequencing runs. In addition, CASAVA automatically generates a range of statistics, such as mean depth and percentage chromosome coverage, to enable comparison with previous builds or other samples. CASAVA analyzes sequencing reads in three stages: * FASTQ file generation and demultiplexing * Alignment to a reference genome * Variant detection and counting | gene, genetic, genomic, linux |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SoftCite |
Free, Available for download, Freely available | nlx_154257, OMICS_01123 | http://www.illumina.com/software/genome_analyzer_software.ilmn | SCR_001802 | Consensus Assessment of Sequence And VAriation | 2026-09-12 01:02:26 | 1960 | ||||||
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POLYMUTT Resource Report Resource Website 1+ mentions |
POLYMUTT (RRID:SCR_002051) | Polymutt | software application, software resource | Software program that implemented a likelihood-based framework for calling single nucleotide variants and detecting de novo point mutation events in families for next-generation sequencing data. The program takes as input genotype likelihood format (GLF) files which can be generated following the Creation of GLF files instruction and outputs the result in the (VCF) format. The variant calling and de novo mutation detection are modelled jointly within families and can handle both nuclear and extended pedigrees without consanguinity loops. The input is a set of GLF files for each of family members and the relationships are specified through the .ped file. (entry from Genetic Analysis Software) | gene, genetic, genomic, next-generation sequencing, mutation, de novo point mutation, single nucleotide variant |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: University of Michigan; Ann Arbor; USA |
PMID:23055937 | Free, Available for download, Freely available | OMICS_00088, nlx_154539 | SCR_002051 | POLYmorphism and de novo MUTaTion call in families with sequencing data | 2026-09-12 01:02:27 | 3 | ||||||
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EIGENSOFT/EIGENSTRAT Resource Report Resource Website 1+ mentions |
EIGENSOFT/EIGENSTRAT (RRID:SCR_001357) | EIGENSOFT/EIGENSTRAT | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, linux | is listed by: Genetic Analysis Software | Free, Available for download, Freely available | nlx_154296 | http://www.hsph.harvard.edu/faculty/alkes-price/software/ | SCR_001357 | 2026-09-12 01:02:26 | 3 | |||||||
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BIRDSUITE Resource Report Resource Website 10+ mentions |
BIRDSUITE (RRID:SCR_001794) | Birdsuite | software application, software resource | Open-source set of tools to detect and report SNP genotypes, common Copy-Number Polymorphisms (CNPs), and novel, rare, or de novo CNVs in samples processed with the Affymetrix platform. While most of the components of the suite can be run individually (for instance, to only do SNP genotyping), the Birdsuite is especially intended for integrated analysis of SNPs and CNVs. | gene, genetic, genomic, snp, genotype, copy number polymorphism, copy number variant, affymetrix |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: Broad Institute |
PMID:18776909 | Free, Available for download, Freely available | OMICS_00705, nlx_154245 | SCR_001794 | 2026-09-12 01:02:26 | 43 | |||||||
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DINDEL Resource Report Resource Website 10+ mentions |
DINDEL (RRID:SCR_001827) | Dindel | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Software program for calling small indels from short-read sequence data ("next generation sequence data"). It is currently designed to handle only Illumina data. Dindel takes BAM files with mapped Illumina read data and enables researchers to detect small indels and produce a VCF file of all the variant calls. It has been written in C++ and can be used on Linux-based and Mac computers (it has not been tested on Windows operating systems). | indel, short-read, next generation sequence, illumina, gene, genetic, genomic, c++, linux, macos, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:20980555 DOI:10.1101/gr.112326.110 |
THIS RESOURCE IS NO LONGER IN SERVICE | , nlx_154283, OMICS_00096, biotools:dindel | https://bio.tools/dindel, https://sources.debian.org/src/dindel/ | http://www.sanger.ac.uk/resources/software/dindel/ | SCR_001827 | Dindel: Accurate indel calls from short-read data | 2026-09-12 01:02:26 | 44 | ||||
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PEDIGRAPH Resource Report Resource Website 10+ mentions |
PEDIGRAPH (RRID:SCR_001938) | Pedigraph | software application, software resource | A pedigree visualization program specifically designed to draw large, complex pedigrees. (entry from Genetic Analysis Software) Options include: * Full pedigree * Summarization * Extraction of individual pedigrees * Inbreeding calculation * Coancestry coefficient calculation * Color control * Drawing size * Page size and margins * Drawing styles | gene, genetic, genomic, c, c++, ms-windows, linux, pedigree, java, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
PMID:14986440 | Acknowledgement required, Copyrighted | biotools:pedigraph, OMICS_00212, nlx_154519 | https://bio.tools/pedigraph | SCR_001938 | 2026-09-12 01:02:27 | 17 | ||||||
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Multipoint Identical-by-descent Method Resource Report Resource Website |
Multipoint Identical-by-descent Method (RRID:SCR_004676) | MIM | software application, software resource | Software application using multipoint IBD method for partitioning genetic variance of quantitative traits to specific chromosome regions using data on nuclear families. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix | is listed by: Genetic Analysis Software | PMID:9433587 | nlx_154482 | SCR_004676 | 2026-09-12 01:02:33 | 0 | ||||||||
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PEDSCRIPT Resource Report Resource Website |
PEDSCRIPT (RRID:SCR_004571) | PEDSCRIPT | software application, software resource | Software tool that allows scripting of simple modifications to pedigree files. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154528 | SCR_004571 | 2026-09-12 01:02:33 | 0 | |||||||||
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PEDPLOT Resource Report Resource Website |
PEDPLOT (RRID:SCR_003843) | PEDPLOT | software application, software resource | Pedigree Plotting Program for the Pedfile Format (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, postscript, unix, (sparc-solaris 2.5/dec unix 4.0/x86-solaris 2.6) | is listed by: Genetic Analysis Software | nlx_154526 | SCR_003843 | 2026-09-12 01:02:31 | 0 | |||||||||
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HAPMIXMAP Resource Report Resource Website |
HAPMIXMAP (RRID:SCR_006066) | HAPMIXMAP | software application, software resource | Software application for modelling extended haplotypes in genetic association studies, similar to the FASTPHASE program. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154391 | SCR_006066 | 2026-09-12 01:02:35 | 0 |
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