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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Wikipedia Resource Report Resource Website 1000+ mentions |
Wikipedia (RRID:SCR_004897) | Wikipedia | narrative resource, data or information resource, wiki, database | Wikipedia is a free, web-based, collaborative, multilingual encyclopedia project supported by the non-profit Wikimedia Foundation. Its 19 million articles (over 3.6 million in English) have been written collaboratively by volunteers around the world, and almost all of its articles can be edited by anyone with access to the site. As of July 2011, there were editions of Wikipedia in 282 languages. Wikipedia was launched in 2001 by Jimmy Wales and Larry Sanger and has become the largest and most popular general reference work on the Internet, ranking around seventh among all websites on Alexa and having 365 million readers. The name Wikipedia was coined by Larry Sanger and is a combination of wiki (a technology for creating collaborative websites, from the Hawaiian word wiki, meaning quick) and encyclopedia. Wikipedia''s departure from the expert-driven style of encyclopedia building and the large presence of unacademic content has been noted several times. Some have noted the importance of Wikipedia not only as an encyclopedic reference but also as a frequently updated news resource because of how quickly articles about recent events appear. Although the policies of Wikipedia strongly espouse verifiability and a neutral point of view, critics of Wikipedia accuse it of systemic bias and inconsistencies (including undue weight given to popular culture), and allege that it favors consensus over credentials in its editorial processes. Its reliability and accuracy are also targeted. A 2005 investigation in Nature showed that the science articles they compared came close to the level of accuracy of Encyclopedia Britannica and had a similar rate of serious errors. |
is used by: DBpedia is related to: ImpactStory is related to: WikiProject Clinical Trials is parent organization of: Comparison of web annotation systems is parent organization of: Gene Wiki is parent organization of: Cumulative Distribution Function is parent organization of: Wikibooks |
Wikimedia Foundation | nlx_86719 | SCR_004897 | 2026-02-14 02:00:48 | 1671 | |||||||||
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SEQanswers Wiki Resource Report Resource Website 1+ mentions |
SEQanswers Wiki (RRID:SCR_004810) | SEQwiki | software repository, data or information resource, wiki, software resource, narrative resource | Wiki forum providing an extensive catalogue of manually categorized analysis tools, technologies and information about service providers, maintained by the members of the SEQanswers community. * Minimum Information about a high-throughput Sequencing Experiment * Software Hub: The place to add to, edit or browse the software database on SEQwiki. * Service Providers: Browse or edit the list of NGS service facilities. * How-to Hub: Mini reviews for the most used tools broken down by common tasks. * Developers Hub: The place to discuss the development of the SEQwiki site and its associated data. See also publishing SEQ*. * Publications: Publication about SEQwiki and selected citations. | sequencing, high-throughput sequencing, service provider, next generation sequencing, next-generation genomics, genomics, data set, wiki, software |
is listed by: 3DVC is listed by: OMICtools has parent organization: SEQanswers |
PMID:22086956 | The community can contribute to this resource | OMICS_01743, nlx_143911 | SCR_004810 | 2026-02-14 02:01:00 | 1 | |||||||
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Inflammatory Breast Cancer Research Foundation Resource Report Resource Website |
Inflammatory Breast Cancer Research Foundation (RRID:SCR_004898) | IBC Research Foundation | portal, data or information resource, funding resource, disease-related portal, topical portal | The Inflammatory Breast Cancer Research Foundation is a non-profit corporation dedicated to the support of research and public awareness. It is dedicated to researching the cause of Inflammatory Breast Cancer, also known as IBC, an advanced and accelerated form of breast cancer usually not detected by mammograms or ultrasounds. Inflammatory breast cancer requires immediate aggressive treatment with chemotherapy prior to surgery and is treated differently than more common types of breast cancer. Our mission is to assist scientists and researchers in their quest to determine the definitive causes of inflammatory breast cancer. The Inflammatory Breast Cancer Research Foundation seeks to assist them in their work so effective and meaningful detection and diagnosis, prevention and treatment can be pursued and achieved. Our Goals Include: * To ignite interest in the study and research of inflammatory breast cancer at every level. From researchers to physicians, educators and scientists, the IBC Research Foundation seeks to support and inspire those seeking to identify the cause(s) of inflammatory breast cancer. * To support research, the purpose of which is to reach an unambiguous definition of inflammatory breast cancer. The clinical/pathological definition in use since the late 1800s with little change in the 1900s is ambiguous and doesn''t result in a diagnosis of all cases of IBC. By using research methods available in the 21st Century, an unambiguous definition is now possible, assuring with high certainty that all cases of IBC will be correctly diagnosed, and possible sub-types of IBC identified, which may lead to better treatment outcomes. * To increase awareness of IBC for primary care physicians, nursing professionals, and medical technicians in order to minimize the time from presentation of symptoms to correct diagnosis of inflammatory breast cancer. * To increase public awareness in an effort to encourage women to seek medical attention for common inflammatory breast cancer symptoms soon after they appear and to empower patients, caregivers, families and friends to pursue meaningful paths in support of diagnosis and treatment of inflammatory breast cancer. | is parent organization of: Inflammatory Breast Cancer Biobank | small tax-deductible voluntary donations | nlx_86933 | SCR_004898 | 2026-02-14 02:01:02 | 0 | |||||||||
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GENEtics Video Resource Report Resource Website |
GENEtics Video (RRID:SCR_004770) | data or information resource, narrative resource, training material, video resource | GENEticS is arap video about genetics. So let''s talk about genes, and I don''t mean trousers, go the lyrics to this catchy rap video created for The GAMY (Genetics and Merthyr Youth) Project. It is one of the many videos, games, and digital media used by researchers at the University of Glamorgan in the United Kingdom use to engage local teenagers in a conversation about genetics. Video produced by Jon Chase (aka Oort Kuiper). | k-12 | has parent organization: University of Glamorgan; South Wales; United Kingdom | nlx_76974 | SCR_004770 | 2026-02-14 02:00:44 | 0 | ||||||||||
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NCBI Sequence Read Archive (SRA) Resource Report Resource Website 5000+ mentions |
NCBI Sequence Read Archive (SRA) (RRID:SCR_004891) | SRA | data repository, storage service resource, data or information resource, service resource, database | Repository of raw sequencing data from next generation of sequencing platforms including including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, Complete Genomics, and Pacific Biosciences SMRT. In addition to raw sequence data, SRA now stores alignment information in form of read placements on reference sequence. Data submissions are welcome. Archive of high throughput sequencing data,part of international partnership of archives (INSDC) at NCBI, European Bioinformatics Institute and DNA Database of Japan. Data submitted to any of this three organizations are shared among them. | sequence, blast, next-generation sequence, alignment, read placement, reference sequence, roche 454 gs system, illumina genome analyzer, applied biosystems solid system, helicos heliscope, complete genomics, pacific biosciences smrt, high-throughput sequencing, data analysis service, gold standard |
is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is listed by: OMICtools is related to: European Nucleotide Archive (ENA) is related to: RecountDB is related to: SRAdb is related to: DDBJ Sequence Read Archive is related to: Bgee: dataBase for Gene Expression Evolution is related to: NCBI BioSample is related to: DDBJ Sequence Read Archive is related to: METAGENOTE has parent organization: NCBI works with: SARS-CoV-2-Sequences works with: Signaling Pathways Project |
NLM | PMID:22009675 PMID:21062823 |
Free, Available for download, Freely available | OMICS_01031, nlx_86174, r3d100010775 | https://doi.org/10.17616/R31S69 | SCR_004891 | Sequence Read Archive, , SRA, NCBI SRA | 2026-02-14 02:01:02 | 6671 | ||||
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Neuroscientists Talk Shop Resource Report Resource Website |
Neuroscientists Talk Shop (RRID:SCR_004806) | Neuroscientists Talk Shop | data or information resource, podcast, narrative resource | The University of Texas at San Antonio''s (UTSA) Neurobiology Podcast, showcasing the current research of internationally renowned guest Neuroscientists. Each episode features a moderated discussion with a cross section of UTSA Neurobiology faculty, highlighting the featured guest''s research, and the state of the art in the field at hand. | neurobiology, neuroscientist | has parent organization: University of Texas at San Antonio; Texas; USA | nlx_151818 | SCR_004806 | 2026-02-14 02:00:47 | 0 | |||||||||
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OpenFlyData.org Resource Report Resource Website |
OpenFlyData.org (RRID:SCR_004807) | OpenFlyData.org | web service, image collection, data or information resource, data access protocol, software resource, database | A cross-database search service for Drosophila gene expression data, including microarray data from FlyAtlas and in situ images from BDGP and Fly-TED. The applications provide different ways to search for and compare gene expression data for the fruit fly Drosophila melanogaster. You may Search Gene Expression Data by Gene, Gene Batch, and by Tissue Expression Profile. A number of Web services (SPARQL endpoints) are provided from this site which may be queried programmatically for data. | microarray, in situ, gene expression, gene, open fly data, openflydata, openflydata, expression, in situ hybridization |
is related to: FlyAtlas: the Drosophila gene expression atlas is related to: Berkeley Drosophila Genome Project has parent organization: FlyWeb Project |
JISC | PMID:20382263 | nlx_79461 | SCR_004807 | open fly data, OpenFlyData, openflydata | 2026-02-14 02:01:01 | 0 | ||||||
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Anatomy Atlases Resource Report Resource Website 1+ mentions |
Anatomy Atlases (RRID:SCR_004888) | Anatomy Atlases | image collection, portal, data or information resource, book, atlas, narrative resource, topical portal | An anatomy digital health sciences library to educate patients, healthcare providers, and students in a free and anonymous manner while using current, authoritative, trustworthy health information. Anatomy Atlases addresses the continuum of anatomy education and may be of use primarily to three distinct populations. It is written for and intended primarily for use by Medical Students, Residents, Fellows, or Attending Physicians studying anatomy. Other Health Care Providers studying anatomy should find it useful. Finally, Patients (including patient''s family members or friends) may find it helpful. Anatomy Textbooks and Anatomy Atlases: * Atlas of Human Anatomy * Atlas of Human Anatomy in Cross Section * Illustrated Encyclopedia of Human Anatomic Variation * Atlas of Microscopic Anatomy - A Functional Approach: Companion to Histology and Neuroanatomy: Second Edition * Anatomy of First Aid - A Case Study Approach * Lessons From a Bone Box Lessons From a Bone Box | anatomy, atlas, first aid, histology, neuroanatomy, bone, anatomic variation | Michael P. D'Alessandro M.D. | nlx_85752 | SCR_004888 | 2026-02-14 02:01:00 | 3 | |||||||||
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Cliniques Universitaires Saint-Luc Cancer Centre Resource Report Resource Website |
Cliniques Universitaires Saint-Luc Cancer Centre (RRID:SCR_004922) | Cliniques Universitaires Saint-Luc Cancer Centre | data or information resource, portal, topical portal, training resource | An essential reference center in Europe and a leader in French-speaking Belgium that treats all types of adult and childhood cancer. They fight against cancer while giving patients comprehensive and humane care. Their quest for excellence is in three main academic fields: clinical care, research and teaching. | cancer, adult human, child, clinical, oncology, research, young human | is parent organization of: Saint-Luc Tumour Bank | Cancer | nlx_143961 | http://www.centreducancer.be/en | SCR_004922 | Centre du Cancer Cliniques Universitaires St-Luc, Cliniques Universitaires Saint-Luc Cancer Center | 2026-02-14 02:00:46 | 0 | ||||||
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PR Resource Report Resource Website |
PR (RRID:SCR_004964) | PR | data or information resource, ontology, controlled vocabulary | An ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. The ontology has a meta-structure encompassing three areas: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp). NOTICE: The PRO ID format has changed from PRO: to PR: (e.g. PRO:000000563 is now PR:000000563). | database, obo, protein |
is listed by: BioPortal has parent organization: Protein Information Resource has parent organization: Georgetown University; Washington D.C.; USA |
NIH ; NIGMS GM080646-01 |
nlx_92849 | SCR_004964 | PRO, Protein Ontology | 2026-02-14 02:01:02 | 0 | |||||||
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Neurodegeneration Research Wiki Resource Report Resource Website |
Neurodegeneration Research Wiki (RRID:SCR_005015) | narrative resource, data or information resource, wiki | A wiki which provides information on neurodegenerative diseases to caregivers, students, and researchers. | neurodegenerative disease, caregiver, student, researcher, proteinaceous aggregate | Public | nlx_98402 | SCR_005015 | 2026-02-14 02:00:47 | 0 | ||||||||||
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University of Iowa; Iowa; USA Resource Report Resource Website 1+ mentions |
University of Iowa; Iowa; USA (RRID:SCR_005011) | UI | university | Public research university in Iowa City, Iowa. Founded in 1847, it is the oldest and the second-largest university in the state. |
is affiliated with: Big Ten Cancer Research Consortium is related to: Clinical and Translational Science Awards Consortium is parent organization of: I/OWA is parent organization of: Hardin MD is parent organization of: Non-Rigid Image Registration Evaluation Project is parent organization of: Brief Psychiatric Rating Scale is parent organization of: University of Iowa Carver College of Medicine; Iowa; USA is parent organization of: Hereditary Hearing Loss Homepage is parent organization of: BRAINSTools is parent organization of: Bayesian Output Analysis Program is parent organization of: Brain Research: Analysis of Images, Networks and Systems is parent organization of: BRAINSDemonWarp is parent organization of: GTRACT is parent organization of: University of Iowa Labs and Facilities is parent organization of: NeuroNEXT is parent organization of: GazeReader is parent organization of: Human Thalamus in 3D Stereotactic Coordinates is parent organization of: University of Iowa Institute of Human Genetics Genomics Division Core Facility hosts: DSHB |
nlx_52860, grid.214572.7, ISNI:0000 0004 1936 8294, Wikidata:Q45133494, Crossref funder ID:100008893 | https://ror.org/036jqmy94 | SCR_005011 | University of Iowa | 2026-02-14 02:00:50 | 8 | ||||||||
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Cover Pages Resource Report Resource Website |
Cover Pages (RRID:SCR_004955) | Cover Pages | portal, data or information resource, interchange format, software resource, markup language, narrative resource, topical portal, database, standard specification | Public reference database supporting the XML family of markup language standards, XML vocabularies, and related structured information standards. It promotes and enables the use of open, interoperable, standards-based solutions which protect digital information and enhance the quality of data processing. The Cover Pages web site provides reference material on enabling technologies compatible with SGML/XML descriptive markup language standards and applications: object modeling, semantic nets, ontologies, authority lists, document production systems, and conceptual modeling. It also supplies references for social aspects of distributed and public sector concerns: privacy, open standards, patented technology embedded in standards, etc. NB. This statement and the resource itself are works in progress, subject to continuous revision. | xml, digital information, open standards | has parent organization: Open Access Series of Imaging Studies | IBM ; ISIS Papyrus ; Microsoft ; Oracle ; Primeton |
Public | nlx_143963 | SCR_004955 | 2026-02-14 02:01:01 | 0 | |||||||
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Wellness Wiki Resource Report Resource Website |
Wellness Wiki (RRID:SCR_004957) | narrative resource, data or information resource, wiki, book | Wellness Wiki is offered to help clarify the complex problems plaguing the U.S. healthcare system and develop sustainable ways to improve the health and well-being of all people. This virtual encyclopedia of the healthcare crisis and potential remedies welcomes your comments! The Wellness Wiki Book (Understanding & Curing American Healthcare: A Wise Way to Better Outcomes and Lower Costs) is available for purchase as a softcover book or pdf download. Table of contents: *Introduction & Executive Summary *Defining the Problem *Examining Three Proposed Solutions *Introducing a New Solution - Overview and Benefits, Wellness-Plus Solution Tactics, Barriers and Drivers to Implementing the Wellness-Plus Solution *Conclusion & Epilogue *Appendix *Wellness Model Technology Blueprint | has parent organization: Wikispaces | nlx_92572 | SCR_004957 | Understanding and Curing the Healthcare Crisis: A Wise Way to Better Outcomes and Lower Costs | 2026-02-14 02:00:49 | 0 | ||||||||||
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MycoBank Resource Report Resource Website 500+ mentions |
MycoBank (RRID:SCR_004950) | MycoBank | data repository, storage service resource, data or information resource, service resource, database | Database documenting mycological nomenclatural novelties (new names and combinations) and associated data, for example descriptions and illustrations. The nomenclatural novelties will each be allocated a unique MycoBank number that can be cited in the publication where the nomenclatural novelty is introduced. These numbers will also be used by the nomenclatural database Index Fungorum, with which MycoBank is associated and will also serve as Life Science Identifiers (LSIDs). Nomenclatural experts will be available to check the validity, legitimacy and linguistic correctness of the proposed names in order to avoid nomenclatural errors; however, no censorship whatsoever, (nomenclatural or taxonomic) will be exerted by MycoBank. Deposited names will remain -when desired- strictly confidential until after publication, and will then be accessible through MycoBank, Index Fungorum, GBIF and other international biodiversity initiatives, where they will further be linked to other databases to realize a species bank that eventually will link all databases of life. MycoBank will (when applicable) provide onward links to other databases containing, for example, living cultures, DNA data, reference specimens and pleomorphic names linked to the same holomorph. Authors intending to publish nomenclatural novelties are encouraged to contribute to this new initiative. For the moment 2 search engines are available from the MycoBank website. The first one permits to search for fungal names (at any rank level), the authority or the MycoBank unique number. The second is dedicated to bibliographic queries related to fungal name''''s publications. MycoBank users willing to deposit their data will have to register so that they willbe able to contact the depositor for specific information (e.g. MycoBank number, possible points of attention regarding the name, actual publication, etc), and to avoid fake entries. | yeast, aspergillus, penicillium, phaeoacremonium, russula, resupinate russulales, mycosphaerella, trichomycete, arthropod, hysteriaceae, mytilinidiaceae, mycology, nomenclature, life science identifier, bibliography, sequence alignment, polyphasic identification, image collection, FASEB list |
is listed by: SoftCite is related to: Index Fungorum |
PMID:24563843 | nlx_91803, r3d100011222 | https://doi.org/10.17616/R39D0Q | SCR_004950 | 2026-02-14 02:01:01 | 743 | |||||||
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BrainLiner Resource Report Resource Website 1+ mentions |
BrainLiner (RRID:SCR_004951) | BrainLiner | data repository, storage service resource, software library, data or information resource, service resource, software toolkit, software application, software resource, database | Portal and tools for sharing and editing neurophysiological and behavioral data for brain-machine interface research. Users can search for existing data or login with their Google, Facebook, or Twitter account and upload new data. Their main focus is on supporting brain-machine interface research, so we encourage users to not just provide recordings of brain activity data, but also information about stimuli, etc., so that statistical relationships can be found between stimuli and/or subject behavior and brain activity. The Matlab tools are for writing, reading, and converting Neuroshare files, the common file format. A free, open source desktop tool for editing neurophysiological data for brain-machine interface research is also available: https://github.com/ATR-DNI/BrainLiner Since data formats aren''''t standardized between programs and researchers, data and analysis programs for data cannot be easily shared. Neuroshare was selected as the common file format. Neuroshare can contain several types of neurophysiological data because of its high flexibility, including analog time-series data and neuronal spike timing. Some applications have plug-ins or libraries available that can read Neuroshare format files, thus making Neuroshare somewhat readily usable. Neuroshare can contain several types of neurophysiological data, but there were no easy tools to convert data into the Neuroshare format, so they made and are providing a Neuroshare Converter Library and Simple Converter using the library. In future work they will make and provide many more useful tools for data sharing. Shared experiments include: EMG signal, Takemiya Exp, Reconstruct (Visual image reconstruction from human brain activity using a combination of multi-scale local image decoders), SPIKE data, Speech Imagery Dataset (Single-trial classification of vowel speech imagery using common spatial patterns), Functional Multineuron Calcium Imaging (fMCI), Rock-paper-scissors (The data was obtained from subject while he make finger-form of rock/paper/scissors). They also have a page at https://www.facebook.com/brainliner where you can contact us | brain-machine interface, brain, behavior, neurophysiology, electromyography, fmri, speech, vision, memory, neuron, eeg, electrocorticography, food tracking task, food tracking, task, meg, mutielectrode, nirs, optical imaging, pet, time-series data, neuronal spike timing, data sharing, manipulation, data set, metadata standard, neuroscience, matlab |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Neuroshare - Open data specifications and software for neurophysiology has parent organization: ATR; Kyoto; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:26858636 | GNU General Public License, The community can contribute to this resource | nlx_91840 | SCR_004951 | BrainLiner.jp | 2026-02-14 02:00:49 | 7 | |||||
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Pythia Resource Report Resource Website 10+ mentions |
Pythia (RRID:SCR_004952) | software resource | Pythia is an open source thermodynamically oriented primer design python module. Pythia can be used in two ways. 1. Executable binaries only: under windows with cygwin and python 2.5 (built with mingw, that comes with the cygwin release). These executables allow the user to index DNA files for primer specificity search, design one primer pair per region, and tile regions with PCR amplicons. 2. A python module: under windows with cygwin, python2.5, numpy, swig, and mingw, or under linux with python2.4 or later, numpy, and swig (everything but numpy should be pre-installed on a normal linux system). The module gets you everything that the binaries get you, in a more pythonic framework. This package also includes modules for computing DNA binding and folding energies using the partition function approach with publicly available thermodynamic data. Usage documentation is in the downloads. | has parent organization: SourceForge | PMID:19528077 | nlx_91969 | SCR_004952 | 2026-02-14 02:01:02 | 42 | ||||||||||
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SLIQ Resource Report Resource Website 1+ mentions |
SLIQ (RRID:SCR_005003) | SLIQ | software resource | Software for simple linear inequalities based Mate-Pair reads filtering and scaffolding. A set of simple linear inequalities (SLIQ) derived from the geometry of contigs on the line that can be used to predict the relative positions and orientations of contigs from individual mate pair reads and thus produce a contig digraph. The SLIQ inequalities can also filter out unreliable mate pairs and can be used as a pre-processing step for any scaffolding algorithm. This tool filters mate pairs and then produces a Directed Contig Graph (contig diGraph). Also provided is a Naive scaffolder that can then produce scaffolds out of the contig diGraph. | python, scaffolding, contig position, contig orientation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Rutgers University; New Jersey; USA |
PMID:23057825 | biotools:sliq, OMICS_00048 | https://bio.tools/sliq | SCR_005003 | Simple linear inequalities, SLiQ: Simple linear inequalities based Mate-Pair reads filtering and scaffolding | 2026-02-14 02:01:03 | 3 | ||||||
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Protein Data Bank Markup Language Resource Report Resource Website 1+ mentions |
Protein Data Bank Markup Language (RRID:SCR_005085) | PDBML | data or information resource, interchange format, markup language, narrative resource, standard specification | Markup Language that provides a representation of PDB data in XML format. The description of this format is provided in XML schema of the PDB Exchange Data Dictionary. This schema is produced by direct translation of the mmCIF format PDB Exchange Data Dictionary Other data dictionaries used by the PDB have been electronically translated into XML/XSD schemas and these are also presented in the list below. * PDBML data files are provided in three forms: ** fully marked-up files, ** files without atom records ** files with a more space efficient encoding of atom records * Data files in PDBML format can be downloaded from the RCSB PDB website or by ftp. * Software tools for manipulating PDB data in XML format are available. | xml |
is related to: RCSB PDB Software Tools has parent organization: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
NSF ; NIGMS ; DOE ; NLM ; NCI ; NCRR ; NIBIB ; NINDS |
PMID:15509603 | nlx_144096 | SCR_005085 | PDBML: Protein Data Bank Markup Language | 2026-02-14 02:01:03 | 2 | ||||||
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cortex var Resource Report Resource Website 1+ mentions |
cortex var (RRID:SCR_005081) | cortex_var | software resource | A tool for genome assembly and variation analysis from sequence data. You can use it to discover and genotype variants on single or multiple haploid or diploid samples. If you have multiple samples, you can use Cortex to look specifically for variants that distinguish one set of samples (eg phenotype=X, cases, parents, tumour) from another set of samples (eg phenotype=Y, controls, child, normal). cortex_var features * Variant discovery by de novo assembly - no reference genome required * Supports multicoloured de Bruijn graphs - have multiple samples loaded into the same graph in different colours, and find variants that distinguish them. * Capable of calling SNPs, indels, inversions, complex variants, small haplotypes * Extremely accurate variant calling - see our paper for base-pair-resolution validation of entire alleles (rather than just breakpoints) of SNPs, indels and complex variants by comparison with fully sequenced (and finished) fosmids - a level of validation beyond that demanded of any other variant caller we are aware of - currently cortex_var is the most accurate variant caller for indels and complex variants. * Capable of aligning a reference genome to a graph and using that to call variants * Support for comparing cases/controls or phenotyped strains * Typical memory use: 1 high coverage human in under 80Gb of RAM, 1000 yeasts in under 64Gb RAM, 10 humans in under 256 Gb RAM | genome assembly, variation analysis, sequence, variation, genotype variant, haploid, diploid, snp, indel, inversion, variant, haplotype, de novo assembly, genotyping, variant-calling, population analysis, population assembly |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Wellcome Trust Centre for Human Genetics |
PMID:22231483 | GNU General Public License, v3, Acknowledgement requested | OMICS_00056 | SCR_005081 | cortex_var - for variant and population assembly | 2026-02-14 02:01:03 | 3 |
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
