tool_and_resource_list.yml

- description: The 1+ Million Genomes (1+MG) initiative aims to enable secure access to genomics and the corresponding clinical data across Europe for better research, personalised healthcare and health policy making. Since the Digital Day 2018, 25 EU countries, the UK and Norway signed Member States declaration on stepping up efforts towards creating a European data infrastructure for genomic data and implementing common national rules enabling federated data access. The initiative forms part of the EU's agenda for the Digital Transformation of Health and Care and is aligned with the goals of the European Health Data Space.
  id: 1-million-genomes
  name: 1+ Million Genomes (1+MG)
  registry:
    tess: 1+ Million Genomes
  url: https://digital-strategy.ec.europa.eu/en/policies/1-million-genomes
- description: Asymptomatic COVID-19 in Education (ACE) Cohort
  id: ace-cohort
  name: ACE Cohort
  registry:
    tess: ACE Cohort
  url: https://co-connect.ac.uk/ace-cohort/
- description: Responsible sharing of biomedical data and biospecimens via the Automatable Discovery and Access Matrix (ADA-M). The Automatable Discovery and Access Matrix (ADA-M) provides a standardized way to unambiguously represent the conditions related to data discovery and access. By adopting ADA-M, data custodians can generally describe what their data are (the Header section), who can access them (the Permissions section), terms related to their use (the Terms section), and special conditions (the Meta-Conditions). By doing so, data custodians can participate in data sharing and collaboration by making meta information about their data computer-readable and hence directly available for digital communication, searching and automation activities.
  id: ada-m
  name: ADA-M
  registry:
    biotools: ada-m
  url: https://github.com/ga4gh/ADA-M
- description: ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes.
  id: annovar
  name: ANNOVAR
  registry:
    biotools: annovar
  url: https://github.com/WGLab/doc-ANNOVAR
- description: ArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. It includes gene expression data from microarray and high throughput sequencing studies. Data is collected to MIAME and MINSEQE standards. Experiments are submitted directly to ArrayExpress or are imported from the NCBI GEO database.
  id: arrayexpress
  name: ArrayExpress
  registry:
    biotools: arrayexpress
    fairsharing: 6k0kwd
    tess: ArrayExpress
  url: https://www.ebi.ac.uk/arrayexpress/
- description: With Arvados, bioinformaticians run and scale compute-intensive workflows, developers create biomedical applications, and IT administrators manage large compute and storage resources.
  id: arvados
  name: Arvados
  url: https://arvados.org/
- description: The Beyond 1 Million Genomes (B1MG) project is helping to create a network of genetic and clinical data across Europe. The project provides coordination and support to the 1+ Million Genomes Initiative (1+MG). This initiative is a commitment of 24 EU countries, the UK and Norway to give cross-border access to one million sequenced genomes by 2022.
  id: beyond-1-million-genomes
  name: Beyond 1 Million Genomes (B1MG)
  url: https://b1mg-project.eu/
- description: Beacon v2 is a protocol/specification established by the Global Alliance for Genomics and Health initiative (GA4GH) that defines an open standard for federated discovery of genomic data and associated information in biomedical research and clinical applications.
  id: beacon
  name: Beacon v2
  registry:
    biotools: beacon
    fairsharing: 6fba91
    tess: Beacon v2
  url: http://docs.genomebeacons.org/
- description: BioGRID is a comprehensive biomedical repository for curated protein, genetic and chemical interactions
  id: biogrid
  name: BioGRID
  registry:
    biotools: biogrid
    fairsharing: lKaOme
  url: https://github.com/BioGRID
- description: BioSamples stores and supplies descriptions and metadata about biological samples used in research and development by academia and industry. Samples are either 'reference' samples (e.g. from 1000 Genomes, HipSci, FAANG) or have been used in an assay database such as the European Nucleotide Archive (ENA) or ArrayExpress. It provides links to assays and specific samples, and accepts direct submissions of sample information.
  id: biosamples
  name: BioSamples
  registry:
    biotools: biosamples
    fairsharing: ewjdq6
    tess: BioSamples
  url: https://www.ebi.ac.uk/biosamples/
- description: Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step.
  id: bismark
  name: Bismark
  registry:
    biotools: bismark
    tess: Bismark
  url: https://github.com/FelixKrueger/Bismark
- description: Git based code hosting and collaboration tool, built for teams.
  id: bitbucket
  name: Bitbucket
  registry:
    fairsharing: fc3431
  url: https://bitbucket.org/
- description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
  id: bowtie2
  name: Bowtie2
  registry:
    biotools: bowtie2
    tess: Bowtie2
  url: https://github.com/BenLangmead/bowtie2
- description: BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
  id: bwa
  name: BWA
  registry:
    biotools: bwa
    tess: BWA
  url: https://github.com/lh3/bwa
- description: Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing.
  id: canu
  name: Canu
  registry:
    biotools: canu
  url: https://github.com/marbl/canu
- description: CESSDA Vocabulary Service enables users to discover, browse, and download controlled vocabularies in a variety of languages. The service is provided by the Consortium of European Social Science Data Archives (CESSDA). The majority of the source (English) vocabularies included in the service have been created by the DDI Alliance. The Data Documentation Initiative (DDI) is an international standard for describing data produced by surveys and other observational methods in the social, behavioural, economic, and health sciences.
  id: cessda-vocabulary-service
  name: CESSDA Vocabulary Service
  registry:
    fairsharing: 5c7cec
  url: https://vocabularies.cessda.eu/about
- description: ClustalW is a progressive multiple sequence alignment tool to align a set of sequences by repeatedly aligning pairs of sequences and previously generated alignments.
  id: clustalw
  name: ClustalW
  registry:
    biotools: clustalw
    tess: ClustalW
  url: https://github.com/coldfunction/CUDA-clustalW
- description: An open standard for describing workflows that are build from command line tools
  id: common-workflow-language
  name: Common Workflow Language (CWL)
  registry:
    fairsharing: 8y5ayx
    tess: Common Workflow Language (CWL)
  url: https://www.commonwl.org/
- description: COMP Superscalar (COMPSs) is a task-based programming model which aims to ease the development of applications for distributed infrastructures, such as large High-Performance clusters (HPC), clouds and container managed clusters.
  id: compss
  name: COMPSs
  registry:
    biotools: compss
  url: https://compss-doc.readthedocs.io/en/stable/
- description: The COVID-19 Data Portal enables researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research. The portal includes relevant datasets submitted to EMBL-EBI as well as other major centres for biomedical data. The COVID-19 Data Portal is the primary entry point into the functions of a wider project, the European COVID-19 Data Platform.
  id: covid-19-data-portal
  name: COVID-19 Data Portal
  registry:
    biotools: covid-19-data-portal
    fairsharing: f3b7a9
    tess: COVID-19 Data Portal
  url: https://www.covid19dataportal.org/
- description: A platform allowing for browsing SARS-CoV-2 variability at the genome, amino acid, structural, and motif levels
  id: crg-covid-19-viral-beacon
  name: CRG COVID-19 Viral Beacon
  url: https://covid19beacon.crg.eu/
- description: Cromwell is a Workflow Management System geared towards scientific workflows.
  id: cromwell
  name: Cromwell
  url: https://cromwell.readthedocs.io/en/stable/tutorials/FiveMinuteIntro/
- description: Reference implementation to provide comprehensive validation of CWL files as well as provide other tools related to working with CWL.
  id: cwltool
  name: cwltool
  url: https://pypi.org/project/cwltool/
- description: Cytoscape provides a solid platform for network visualization and analysis
  id: cytoscape
  name: Cytoscape
  registry:
    biotools: cytoscape
    tess: Cytoscape
  url: https://apps.cytoscape.org/
- description: The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand the biological meaning behind large lists of genes.
  id: david
  name: DAVID
  registry:
    biotools: david_bioinformatics_resources
    tess: DAVID
  url: https://david.ncifcrf.gov/
- description: The Database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. Such studies include genome-wide association studies, medical sequencing, molecular diagnostic assays, as well as association between genotype and non-clinical traits.
  id: dbgap
  name: dbGaP
  registry:
    biotools: dbgap
    fairsharing: 88v2k0
    tess: dbGaP
  url: https://www.ncbi.nlm.nih.gov/gap/
- description: A comprehensive database of transcript-specific functional predictions and annotations for human non-synonymous and splice-site SNVs
  id: dbnsfp
  name: dbNSFP
  registry:
    biotools: dbnsfp
  url: https://github.com/shiquan/bcfanno/blob/master/Documentation/database/dbNSFP.md
- description: DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file.
  id: deepvariant
  name: DeepVariant
  registry:
    biotools: deepvariant
  url: https://github.com/google/deepvariant
- description: Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read and long-read massively parallel sequencing data.
  id: delly
  name: Delly
  registry:
    biotools: delly2
  url: https://github.com/dellytools/delly
- description: Differential gene expression analysis based on the negative binomial distribution
  id: deseq2
  name: DESeq2
  registry:
    biotools: deseq2
    tess: DESeq2
  url: https://bioconductor.org/packages/release/bioc/html/DESeq2.html
- description: DMP online is an online planning tool to help you write an effective DMP based on an institutional or funder template.
  id: dmp-online
  name: DMP Online
  registry:
    tess: DMP Online
  url: https://dmptool.org/
- description: Docker is a software for the execution of applications in virtualized environments called containers. It is linked to DockerHub, a library for sharing container images
  id: docker
  name: Docker
  registry:
    fairsharing: afc2b3
    fairsharing-coll: bsg-d001254
    tess: Docker
  url: https://www.docker.com/
- description: DRAGEN-GATK Best Practices contains open-source workflows that are compatible between Illumina's platforms and mainstream infrastructure.
  id: dragen-gatk
  name: Dragen-GATK
  url: https://gatk.broadinstitute.org/hc/en-us/articles/360045944831
- description: 'Dryad is an open-source, community-led data curation, publishing, and preservation platform for CC0 publicly available research data. Dryad has a long-term data preservation strategy, and is a Core Trust Seal Certified Merritt repository with storage in US and EU at the San Diego Supercomputing Center, DANS, and Zenodo. While data is undergoing peer review, it is embargoed if the related journal requires / allows this. Dryad is an independent non-profit that works directly with: researchers to publish datasets utilising best practices for discovery and reuse; publishers to support the integration of data availability statements and data citations into their workflows; and institutions to enable scalable campus support for research data management best practices at low cost. Costs are covered by institutional, publisher, and funder members, otherwise a one-time fee of $120 for authors to cover cost of curation and preservation. Dryad also receives direct funder support through
    grants.'
  id: dryad
  name: Dryad
  registry:
    fairsharing: wkggtx
  url: http://datadryad.org/
- description: The European Bioinformatics Institute is a bioinformatics research center that is part of the European Molecular Biology Laboratory and is located in Hinxton, England. The institution combines intense research activity with the development and maintenance of a set of bioinformatics lines, services and databases.
  id: ebi
  name: EBI
  registry:
    tess: EBI
  url: https://www.ebi.ac.uk/
- description: Empirical Analysis of Digital Gene Expression Data in R
  id: edger
  name: EdgeR
  registry:
    biotools: edger
    tess: EdgeR
  url: https://bioconductor.org/packages/release/bioc/html/edgeR.html
- description: The European Genome-phenome Archive (EGA) is a service for permanent archiving and sharing of personally identifiable genetic, phenotypic, and clinical data generated for the purposes of biomedical research projects or in the context of research-focused healthcare systems. Access to data must be approved by the specified Data Access Committee (DAC).
  id: ega
  name: European Genome-phenome Archive (EGA)
  registry:
    biotools: ega
    fairsharing: mya1ff
    tess: European Genome-phenome Archive (EGA)
  url: https://ega-archive.org/
- description: 'The European Language Social Science Thesaurus (ELSST) is a broad-based, multilingual thesaurus for the social sciences. It is owned and published by the Consortium of European Social Science Data Archives (CESSDA) and its national Service Providers. The thesaurus consists of over 3,300 concepts and covers the core social science disciplines: politics, sociology, economics, education, law, crime, demography, health, employment, information, communication technology, and environmental science. ELSST is used for data discovery within CESSDA and facilitates access to data resources across Europe, independent of domain, resource, language, or vocabulary. ELSST is currently available in 16 languages: Danish, Dutch, Czech, English, Finnish, French, German, Greek, Hungarian, Icelandic, Lithuanian, Norwegian, Romanian, Slovenian, Spanish, and Swedish'
  id: european-language-social-science-thesaurus
  name: European Language Social Science Thesaurus (ELSST)
  registry:
    fairsharing: acd824
  url: https://elsst.cessda.eu/
- description: Galaxy tool wrapper of the ENA upload CLI to submit experimental data and respective metadata to the European Nucleotide Archive (ENA).
  id: ena-upload-tool
  name: ENA upload Galaxy tool
  url: https://toolshed.g2.bx.psu.edu/repository?repository_id=0db04aa13ef9d2f8
- description: Command line tool (CLI) allowing easy submission of data and respective metadata to the European Nucleotide Archive (ENA) using tabular files or an excel spreadsheet. The tool allows programatic submission of all ENA objects (study, sample, run and experiment) without the need of logging in to the Webin interface. This also includes client side validation using ENA checklists and releasing the ENA objects.
  id: ena-upload-cli
  name: ENA upload CLI
  url: https://github.com/usegalaxy-eu/ena-upload-cli
- description: Galaxy wrapper to submit consensus sequences to ENA in an interactive way. The tool has the Webin-CLI script of ENA at its core and supports all sample checklists.
  id: ena-webin-cli
  name: ENA Webin CLI
  url: https://toolshed.g2.bx.psu.edu/repository?repository_id=dfa4f0fc31027b52
- description: Functional Enrichment Analysis and Network Construction
  id: enrichr
  name: Enrichr
  registry:
    biotools: enrichr
  url: https://github.com/guokai8/EnrichR
- description: The Estonian Biobank has established a population-based biobank of Estonia with a current cohort size of more than 200,000 individuals (genotyped with genome-wide arrays), reflecting the age, sex and geographical distribution of the adult Estonian population. Considering the fact that about 20% of Estonia's adult population has joined the programme, it is indeed a database that is very important for the development of medical science both domestically and internationally.
  id: estonian-biobank
  name: Estonian Biobank
  url: https://genomics.ut.ee/en/content/estonian-biobank
- description: Estonian instance of the COVID-19 Data Portal. Among other information, served Estonian SARS-CoV-2 sequencing dashboards.
  id: estonian-covid-19-data-portal
  name: Estonian COVID-19 Data Portal
  url: https://covid19dataportal.ee/
- description: Provides a record of the nucleotide sequencing information. It includes raw sequencing data, sequence assembly information and functional annotation.
  id: european-nucleotide-archive
  name: European Nucleotide Archive (ENA)
  registry:
    biotools: ena
    fairsharing: dj8nt8
    tess: European Nucleotide Archive (ENA)
  url: https://www.ebi.ac.uk/ena/browser/home
- description: FAIRsharing is a FAIR-supporting resource that provides an informative and educational registry on data standards, databases, repositories and policy, alongside search and visualization tools and services that interoperate with other FAIR-enabling resources. fairsharing guides consumers to discover, select and use standards, databases, repositories and policy with confidence, and producers to make their resources more discoverable, more widely adopted and cited. Each record in fairsharing is curated in collaboration with the maintainers of the resource themselves, ensuring that the metadata in the fairsharing registry is accurate and timely. Every record is manually reviewed at least once a year. Records can be collated into collections, based on a project, society or organisation, or Recommendations, where they are collated around a policy, such as a journal or funder data policy.
  id: fairsharing
  name: FAIRsharing
  registry:
    fairsharing: 2abjs5
    tess: FAIRsharing
  url: https://fairsharing.org/
- description: Figshare is a generalist, subject-agnostic repository for many different types of digital objects that can be used without cost to researchers. Data can be submitted to the central figshare repository (described here), or institutional repositories using the figshare software can be installed locally, e.g. by universities and publishers. Metadata in figshare is licenced under is CC0. figshare has also partnered with DuraSpace and Chronopolis to offer further assurances that public data will be archived under the stewardship of Chronopolis. figshare is supported through Institutional, Funder, and Governmental service subscriptions.
  id: figshare
  name: Figshare
  registry:
    fairsharing: drtwnh
    tess: Figshare
  url: http://figshare.com/
- description: Flye is a de novo assembler for single-molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies.
  id: flye
  name: Flye
  registry:
    biotools: Flye
    tess: Flye
  url: https://github.com/fenderglass/Flye
- description: FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, MNPs, and complex events smaller than the length of a short-read sequencing alignment.
  id: freebayes
  name: FreeBayes
  registry:
    biotools: freebayes
    tess: FreeBayes
  url: https://github.com/freebayes/freebayes
- description: The metadata model for GA4GH, an international coalition of both public and private interested parties, formed to enable the sharing of genomic and clinical data.
  id: ga4gh
  name: GA4GH
  registry:
    biotools: ga4gh
    fairsharing: 2tpx4v
    tess: GA4GH
  url: https://github.com/ga4gh/schemas
- description: Open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.
  id: galaxy
  name: Galaxy
  registry:
    biotools: galaxy
    tess: Galaxy
  url: https://galaxyproject.org
- description: The European Galaxy server. Provides access to thousands of tools for scalable and reproducible analysis.
  id: galaxy-europe
  name: Galaxy Europe
  url: https://usegalaxy.eu/
- description: The University of Tartu Galaxy instance. Enables local university users to run their analyses in the Galaxy environment. Was heavily used during the KoroGenoEST sequencing studies.
  id: galaxy-university-of-tartu
  name: Galaxy University of Tartu
  url: https://galaxy.hpc.ut.ee/
- description: GenBank is the NIH genetic sequence database of annotated collections of all publicly available DNA sequences.
  id: genbank
  name: GenBank
  registry:
    biotools: genbank
    fairsharing: 9kahy4
    tess: GenBank
  url: https://www.ncbi.nlm.nih.gov/genbank/
- description: GeneMANIA helps you predict the function of your favourite genes and gene sets.
  id: genemania
  name: GeneMANIA
  registry:
    biotools: genemania
    tess: GeneMANIA
  url: https://github.com/GeneMANIA/genemania
- description: The Genomic Data Infrastructure (GDI) project is enabling access to genomic and related phenotypic and clinical data across Europe. It is doing this by establishing a federated, sustainable and secure infrastructure to access the data. It builds on the outputs of the Beyond 1 Million Genomes (B1MG) project and is realising the ambition of the 1+Million Genomes (1+MG) initiative.
  id: genomic-data-infrastructure
  name: Genomic Data Infrastructure (GDI)
  url: https://gdi.onemilliongenomes.eu/
- description: The Gene Expression Omnibus (GEO) is a public repository that archives and freely distributes microarray, next-generation sequencing, and other forms of high-throughput functional genomic data submitted by the scientific community. Accepts next generation sequence data that examine quantitative gene expression, gene regulation, epigenomics or other aspects of functional genomics using methods such as RNA-seq, miRNA-seq, ChIP-seq, RIP-seq, HiC-seq, methyl-seq, etc. GEO will process all components of your study, including the samples, project description, processed data files, and will submit the raw data files to the Sequence Read Archive (SRA) on the researchers behalf. In addition to data storage, a collection of web-based interfaces and applications are available to help users query and download the studies and gene expression patterns stored in GEO.
  id: geo
  name: GEO
  registry:
    fairsharing: 5hc8vt
    tess: GEO
  url: https://www.ncbi.nlm.nih.gov/geo/
- description: ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.
  id: ggplot2
  name: ggplot2
  registry:
    biotools: ggplot2
    tess: ggplot2
  url: https://github.com/tidyverse/ggplot2
- description: GitHub is a versioning system, used for sharing code, as well as for sharing of small data.
  id: github
  name: GitHub
  registry:
    fairsharing: c55d5e
    fairsharing-coll: bsg-d001160
    tess: GitHub
  url: https://github.com/
- description: GitLab is an open source end-to-end software development platform with built-in version control, issue tracking, code review, CI/CD, and more. Self-host GitLab on your own servers, in a container, or on a cloud provider.
  id: gitlab
  name: GitLab
  registry:
    fairsharing: 530e61
    tess: GitLab
  url: https://about.gitlab.com/
- description: GO is to perform enrichment analysis on gene sets.
  id: go
  name: GO
  registry:
    biotools: go
    tess: GO
  url: http://geneontology.org/docs/go-enrichment-analysis/
- description: GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.
  id: gridss
  name: GRIDSS
  registry:
    biotools: gridss
  url: https://github.com/PapenfussLab/gridss
- description: Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states
  id: gsea
  name: GSEA
  registry:
    biotools: gsea
    tess: GSEA
  url: https://www.gsea-msigdb.org/gsea/index.jsp
- description: The Genotype-Tissue Expression (GTEx) project is an ongoing effort to build a comprehensive public resource to study tissue-specific gene expression and regulation. Samples were collected from 53 non-diseased tissue sites across nearly 1000 individuals, primarily for molecular assays including WGS, WES, and RNA-Seq. Remaining samples are available from the GTEx Biobank. The GTEx Portal provides open access to data including gene expression, QTLs, and histology images.
  id: gtex
  name: GTEx
  registry:
    biotools: gtex
    fairsharing: 293c15
    tess: GTEx
  url: https://gtexportal.org/
- description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (whole-genome, transcriptome, and exome sequencing data) to a population of human genomes (as well as to a single reference genome).
  id: hisat2
  name: HISAT2
  registry:
    biotools: hisat2
    tess: HISAT2
  url: https://github.com/DaehwanKimLab/hisat2
- description: The Integrative Genomics Viewer (IGV) is a high-performance, easy-to-use, interactive tool for the visual exploration of genomic data.
  id: igv
  name: IGV
  registry:
    biotools: igvr
    tess: IGV
  url: https://software.broadinstitute.org/software/igv/
- description: IntAct (Molecular Interaction Database) Website
  id: intact
  name: IntAct
  registry:
    biotools: intact
    fairsharing: d05nwx
    tess: IntAct
  url: https://github.com/intact-portal
- description: A set of annotation maps for Kyoto encyclopedia of genes and genomes (KEGG)
  id: kegg
  name: KEGG
  registry:
    biotools: kegg
    tess: KEGG
  url: https://www.bioconductor.org/packages//2.11/data/annotation/html/KEGG.db.html
- description: LimeSurvey is a free and open source advanced online survey system to create online surveys.
  id: limesurvey
  name: LimeSurvey
  url: https://www.limesurvey.org/
- description: A probabilistic framework for structural variant discovery.
  id: lumpy
  name: Lumpy
  registry:
    biotools: lumpy
  url: https://github.com/arq5x/lumpy-sv
- description: Model-based Analysis of ChIP-Seq (MACS), for identifying transcript factor binding sites.
  id: macs
  name: MACS
  registry:
    biotools: macs
    tess: MACS
  url: https://github.com/macs3-project/MACS
- description: MAFFT is a multiple sequence alignment program
  id: mafft
  name: MAFFT
  registry:
    biotools: MAFFT
  url: https://github.com/GSLBiotech/mafft
- description: Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads.
  id: manta
  name: Manta
  registry:
    biotools: manta
  url: https://github.com/Illumina/manta
- description: Matplotlib is a comprehensive library for creating static, animated, and interactive visualizations in Python.
  id: matplotlib
  name: matplotlib
  registry:
    biotools: matplotlib
  url: https://github.com/matplotlib/matplotlib
- description: MetaboAnalyst is a comprehensive platform dedicated for metabolomics data analysis via user-friendly, web-based interface.
  id: metaboanalyst
  name: MetaboAnalyst
  registry:
    biotools: metaboanalyst
    tess: MetaboAnalyst
  url: https://www.metaboanalyst.ca/
- description: Cleans metagenomic reads to remove adapters, low-quality bases and host (e.g. human) contamination.
  id: metagen-fastqc
  name: Metagen-FastQC
  url: https://github.com/Finn-Lab/Metagen-FastQC
- description: methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing.
  id: methylkit
  name: MethylKit
  registry:
    biotools: methylkit
  url: https://github.com/al2na/methylKit
- description: Base resolution DNA methylation data analysis
  id: methylpipe
  name: methylPipe
  registry:
    biotools: methylpipe
  url: https://bioconductor.riken.jp/packages/3.1/bioc/html/methylPipe.html
- description: A computational platform for high-resolution mass spectrometry-based metabolomics
  id: metsign
  name: MetSign
  url: https://pubmed.ncbi.nlm.nih.gov/21932828/
- description: MIABIS represents the minimum information required to initiate collaborations between biobanks and to enable the exchange of biological samples and data. The aim is to facilitate the reuse of bio-resources and associated data by harmonizing biobanking and biomedical research.
  id: miabis
  name: MIABIS
  registry:
    fairsharing: s0jj2t
  url: http://bbmri-wiki.wikidot.com/en:dataset
- description: MUSCLE is widely-used software for making multiple alignments of biological sequences.
  id: muscle
  name: MUSCLE
  registry:
    biotools: muscle
    tess: MUSCLE
  url: https://github.com/rcedgar/muscle
- description: MZmine 3 is an open-source software for mass-spectrometry data processing, with the main focus on LC-MS data.
  id: mzmine
  name: Mzmine
  registry:
    biotools: mzmine
  url: http://mzmine.github.io/
- description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.
  id: ncbi
  name: NCBI
  registry:
    tess: NCBI
  url: https://www.ncbi.nlm.nih.gov/
- description: Nextflow is a framework for data analysis workflow execution
  id: nextflow
  name: Nextflow
  registry:
    biotools: nextflow
    tess: Nextflow
  url: https://www.nextflow.io/
- description: Estonian local instance of the Nextstrain Auspice application that serves SARS-CoV-2 phylogenetic data
  id: nextstrain-auspice
  name: Nextstrain Auspice
  url: https://auspice.biit.cs.ut.ee/ncov/est
- description: Omics Integrator is a package designed to integrate proteomic data, gene expression data and/or epigenetic data using a protein-protein interaction network.
  id: omicsgenerator
  name: Omicsgenerator
  url: https://github.com/fraenkel-lab/OmicsIntegrator
- description: OpenMS is an open-source software C++ library for LC-MS data management and analyses.
  id: openms
  name: OpenMS
  registry:
    biotools: openms
    tess: OpenMS
  url: https://github.com/OpenMS/OpenMS
- description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.
  id: panther
  name: Panther
  registry:
    biotools: panther
    fairsharing: ty3dqs
    tess: Panther
  url: http://www.pantherdb.org/
- description: PhyML is a software package that uses modern statistical approaches to analyse alignments of nucleotide or amino acid sequences in a phylogenetic framework.
  id: phyml
  name: PhyML
  registry:
    biotools: phyml
  url: https://github.com/stephaneguindon/phyml
- description: R Markdown can help to turn your analyses into high quality documents, reports, presentations and dashboards.
  id: r-markdown
  name: R Markdown
  registry:
    tess: R Markdown
  url: https://rmarkdown.rstudio.com/
- description: Shiny is an R package that makes it easy to build interactive web apps straight from R.
  id: r-shiny
  name: R Shiny
  registry:
    tess: R Shiny
  url: https://shiny.rstudio.com/
- description: Implementation of Workflow Execution Service (WES) or so-called Workflow-as-a-Service.
  id: sapporo-wes
  name: Sapporo WES
  registry:
    biotools: sapporo-web
  url: https://github.com/sapporo-wes/sapporo
- description: Redesigned and improved ChIP-seq broad peak calling tool SICER
  id: sicer2
  name: SICER2
  url: https://github.com/zanglab/SICER2
- description: Singularity is a widely-adopted container runtime that implements a unique security model to mitigate privilege escalation risks and provides a platform to capture a complete application environment into a single file (SIF)
  id: singularity
  name: Singularity
  registry:
    tess: Singularity
  url: https://sylabs.io/
- description: Snakemake is a framework for data analysis workflow execution
  id: snakemake
  name: Snakemake
  registry:
    biotools: snakemake
    tess: Snakemake
  url: https://snakemake.readthedocs.io/en/stable/
- description: Genetic variant annotation and functional effect prediction toolbox. It annotates and predicts the effects of genetic variants on genes and proteins.
  id: snpeff
  name: SnpEff
  registry:
    biotools: snpeff
    tess: SnpEff
  url: https://github.com/pcingola/SnpEff
- description: SPAdes is an assembly toolkit containing various assembly pipelines.
  id: spades
  name: SPAdes
  registry:
    biotools: spades
    tess: SPAdes
  url: https://github.com/ablab/spades
- description: The SRA is NIH's primary archive of high-throughput sequencing data and is part of the International Nucleotide Sequence Database Collaboration (INSDC) that includes at the NCBI Sequence Read Archive (SRA), the European Bioinformatics Institute (EBI), and the DNA Database of Japan (DDBJ). Data submitted to any of the three organizations are shared among them. SRA accepts data from all kinds of sequencing projects including clinically important studies that involve human subjects or their metagenomes, which may contain human sequences. These data often have a controlled access via dbGaP (the database of Genotypes and Phenotypes).
  id: sra
  name: SRA
  registry:
    biotools: sra
    fairsharing: g7t2hv
    tess: SRA
  url: http://www.ncbi.nlm.nih.gov/sra
- description: Spliced Transcripts Alignment to a Reference
  id: star
  name: STAR
  registry:
    biotools: star
    tess: STAR
  url: https://github.com/alexdobin/STAR
- description: Container-native workflow manager for hybrid infrastructures
  id: streamflow
  name: StreamFlow
  url: https://streamflow.di.unito.it/
- description: The Cancer Genome Atlas (TCGA) is a comprehensive, collaborative effort led by the National Institutes of Health (NIH) to map the genomic changes associated with specific types of tumors to improve the prevention, diagnosis and treatment of cancer. Its mission is to accelerate the understanding of the molecular basis of cancer through the application of genome analysis and characterization technologies.
  id: tcga
  name: TCGA
  registry:
    fairsharing: m8wewa
    tess: TCGA
  url: https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga
- description: The Data Use Ontology (DUO) describes data use requirements and limitations. DUO allows to semantically tag datasets with restriction about their usage, making them discoverable automatically based on the authorization level of users, or intended usage. This resource is based on the OBO Foundry principles, and developed using the W3C Web Ontology Language. It is used in production by the European Genome-phenome Archive (EGA) at EMBL-EBI and CRG as well as the Broad Institute for the Data Use Oversight System (DUOS).
  id: the-data-use-ontology
  name: The Data Use Ontology (DUO)
  registry:
    fairsharing: 5dnjs2
  url: https://raw.githubusercontent.com/EBISPOT/DUO/master/duo.owl
- description: The toil-cwl-runner command provides cwl-parsing functionality using cwltool, and leverages the job-scheduling and batch system support of Toil.
  id: toil-cwl-runner
  name: toil-cwl-runner
  url: https://toil.readthedocs.io/en/latest/running/cwl.html
- description: An online tool for analyzing and visualizing genomic data. It allows users to add and share annotations.
  id: ucsc-genome-browser
  name: UCSC Genome Browser
  registry:
    biotools: ucsc_genome_browser
    fairsharing: s22qdj
  url: https://genome.ucsc.edu/
- description: Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  id: varscan
  name: VarScan
  registry:
    biotools: varscan
  url: https://github.com/dkoboldt/varscan
- description: VEP (Variant Effect Predictor) predicts the functional effects of genomic variants.
  id: vep
  name: VEP
  registry:
    biotools: vep
    tess: VEP
  url: https://github.com/Ensembl/ensembl-vep
- description: A registry for describing, sharing and publishing scientific computational workflows.
  id: workflowhub
  name: WorkflowHub
  registry:
    biotools: workflowhub
    fairsharing: 07cf72
    tess: WorkflowHub
  url: https://workflowhub.eu
- description: Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT).
  id: wtdbg2
  name: wtdbg2
  registry:
    biotools: wtdbg2
  url: https://github.com/ruanjue/wtdbg2
- description: Metabolomic and lipidomic platform
  id: xcms
  name: XCMS
  registry:
    biotools: xcms
    tess: XCMS
  url: https://xcmsonline.scripps.edu/landing_page.php?pgcontent=mainPage
- description: Zenodo is a generalist research data repository built and developed by OpenAIRE and CERN. It was developed to aid Open Science and is built on open source code. Zenodo helps researchers receive credit by making the research results citable and through OpenAIRE integrates them into existing reporting lines to funding agencies like the European Commission. Citation information is also passed to DataCite and onto the scholarly aggregators. Content is available publicly under any one of 400 open licences (from opendefinition.org and spdx.org). Restricted and Closed content is also supported. Free for researchers below 50 GB/dataset. Content is both online on disk and offline on tape as part of a long-term preservation policy. Zenodo supports managed access (with an access request workflow) as well as embargoing generally and during peer review. The base infrastructure of Zenodo is provided by CERN, a non-profit IGO. Projects are funded through grants.
  id: zenodo
  name: Zenodo
  registry:
    fairsharing: wy4egf
    tess: Zenodo
  url: https://www.zenodo.org/
- description: SANE is a virtual container in which the researcher can analyse sensitive data, while the data owner retains full control.
  id: oddisei-secure-analysis-environment
  name: ODDISEI Secure ANalysis Environment (SANE)
  url: https://odissei-data.nl/en/2022/02/secure-analysis-environment-sane-secure-data-for-social-sciences-and-humanities/
- description: CDC is a one-stop shop for searching and finding European social science data.
  id: cessda-data-catalogue
  name: CESSDA Data Catalogue (CDC)
  registry:
    biotools: cdc
    fairsharing: a12316
  url: https://datacatalogue.cessda.eu/
- description: The COVID-19 SSH Data Portal provides integrated search, discovery, and linking to datasets published on the web relevant for COVID-19-related research in the Social Sciences and Humanities.
  id: eui-covid-19-ssh-data-portal
  name: EUI COVID-19 SSH Data Portal
  registry:
    fairsharing: 97367f
  url: https://covid-19.eui.eu/
- description: RO-Crate is a lightweight approach to packaging research data with their metadata, using schema.org. An RO-Crate is a structured archive of all the items that contributed to the research outcome, including their identifiers, provenance, relations and annotations.
  id: research-object-crate
  name: Research Object Crate (RO-Crate)
  registry:
    fairsharing: wUoZKE
  url: https://w3id.org/ro/crate
- description: Schema.org is a collaborative, community activity with a mission to create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, and beyond.
  id: schema-org
  name: Schema.org
  registry:
    fairsharing: hzdzq8
    tess: Schema.org
  url: https://schema.org
- description: Workflow Execution Service Backend (WfExS-backend) is a high-level orchestrator to run scientific workflows reproducibly.
  id: wfexs
  name: WfExS
  url: https://github.com/inab/WfExS-backend
- description: An RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web. By using DCAT to describe datasets in data catalogs, publishers increase discoverability and enable applications easily to consume metadata from multiple catalogs.
  id: dcat
  name: DCAT
  registry:
    fairsharing: h4j3qm
  url: https://www.w3.org/TR/vocab-dcat-2/
- description: The dutch COVID-19 Data Portal provides researchers with a clear overview of what is available, allow searching for specific data and make access to such data easier when the necessary ethical and legal conditions have been met.
  id: dutch-covid19-data-portal
  name: Dutch COVID-19 Data Portal
  url: https://covid19initiatives.health-ri.nl/p/Dashboard
- description: The Federated EGA is an infrastructure built upon the European Genome-phenome Archive (EGA), an EMBL-EBI and CRG data resource for secure archiving and sharing of human sensitive biomolecular and phenotypic data resulting from biomedical research projects.
  id: fega
  name: Federated EGA
  registry:
    tess: Federated EGA
  url: https://www.covid19dataportal.org/federated-ega
- description: Using technology that builds upon existing EMBL-EBI infrastructure, we provide SARS-CoV-2 Data Hubs to those public health agencies and other scientific groups responsible for generating viral sequence data from the outbreak at national or regional levels.
  id: sars-cov2-data-hubs
  name: SARS-CoV-2 Data Hubs
  url: https://www.covid19dataportal.org/data-hubs
- description: A quality control tool for high throughput sequence data.
  id: fastqc
  name: FASTQC
  registry:
    biotools: fastqc
    tess: FASTQC
  url: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
- description: SAMtools is a suite of programs for interacting with high-throughput sequencing data.
  id: samtools
  name: SAMtools
  registry:
    biotools: samtools
    tess: SAMtools
  url: http://www.htslib.org/
- description: MultiQC searches a given directory for analysis logs and compiles a HTML report.
  id: multiqc
  name: MultiQC
  registry:
    biotools: multiqc
    tess: MultiQC
  url: https://multiqc.info/
- description: VCFtools is a program package designed for working with VCF files.
  id: vcftools
  name: VCFtools
  registry:
    biotools: vcftools
  url: https://vcftools.sourceforge.net/
- description: A web-based platform for sharing viral sequence data, initially for influenza data, and now for other pathogens (including SARS-CoV-2).
  id: gisaid
  name: Global Initiative on Sharing All Influenza Data (GISAID)
  registry:
    fairsharing: 2f7f9f
  url: https://gisaid.org
- description: The Pathogens Portal Cohort Browser presents discovery metadata of infectious disease cohort datasets and provides links to the associated datasets within ELIXIR Core Data Resources; search and filtering functionalities enable users to identify cohort studies of interest in a convenient manner.
  id: pathogens-cohort-browser
  name: Pathogens Portal Cohort Browser
  url: https://www.pathogensportal.org/cohorts
- description: The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication.
  id: biostudies
  name: BioStudies
  registry:
    biotools: biostudies
    fairsharing: mtjvme
    tess: BioStudies
  url: https://www.ebi.ac.uk/biostudies/
- description: The ISARIC-WHO Case Report Forms (CRFs) should be used to collect data on individuals presenting with suspected or confirmed COVID-19, with the aim to standardise clinical data to improve patient care and inform the public health response.
  id: isaric-covid-19-crf
  name: ISARIC COVID-19 Case Report Form
  registry:
    fairsharing: 1ece03
  url: https://isaric.org/document/covid-19-crf/
- description: The Swedish Pathogens Portal was previously known as the Swedish COVID-19 Data Portal. It is the Swedish national node of the Pathogens Portal, aimed at facilitating the sharing of data related to pathogens and pandemic preparedness.
  id: swedish-pathogens-portal
  name: Swedish Pathogens Portal
  registry:
    fairsharing: a085b2
  url: https://pathogens.se
- description: The Pathogens Portal, launched in July 2023, is an invaluable resource for researchers, clinicians, and policymakers who need access to the latest and most comprehensive datasets on pathogens. The portal is a collaborative effort between the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) and partners.
  id: pathogens-portal
  name: Pathogens Portal
  registry:
    fairsharing: a085b2
    tess: Pathogens Portal
  url: https://www.pathogensportal.org
- description: The European Health Data Space is a health specific ecosystem comprised of rules, common standards and practices, infrastructures and a governance framework that aims at empowering individuals through increased digital access to and control of their electronic personal health data, at national level and EU-wide.
  id: ehds
  name: European Health Data Space (EHDS)
  url: https://health.ec.europa.eu/ehealth-digital-health-and-care/european-health-data-space_en
- description: The European Medicines Agency (EMA) is a decentralised agency of the European Union (EU). It is responsible for the scientific evaluation, supervision and safety monitoring of medicines.
  id: ema
  name: European Medicines Agency (EMA)
  url: https://www.ema.europa.eu/en
- description: It is an EU agency aimed at strengthening Europe's defences against infectious diseases. Their mission is to identify, assess and communicate current and emerging threats to human health posed by infectious diseases.
  id: ecdc
  name: European Centre for Disease Prevention and Control (ECDC)
  url: https://www.ecdc.europa.eu/en
- description: The European Health Information Gateway is a platform that provides access to various health information resources and datasets from across Europe, including data on health systems, health determinants, and health outcomes.
  id: info-gateway
  name: The European Health Information Gateway
  url: https://gateway.euro.who.int/en/
- description: ECRIN develops, contributes to, and maintains freely accessible tools that facilitate the identification of clinical trial objects, data sharing, access to regulatory and methodological designs and much more to support researchers looking to conduct multinational clinical research.
  id: ecrin-tools
  name: European Clinical Research Infrastructure Network (ECRIN) tools
  url: https://ecrin.org/tools
- description: The Health Information Portal provides access to population health and healthcare data across Europe.
  id: health-portal
  name: European Health Information Portal
  registry:
    fairsharing: 8690f1
  url: https://www.healthinformationportal.eu/
- description: PHIRI is the roll-out of the research infrastructure on population health information that aims to facilitate and generate the best available evidence for research on health and well-being of populations as impacted by COVID-19.
  id: phiri
  name: Population Health Information Research Infrastructure (PHIRI)
  url: https://www.phiri.eu/
- description: Research at the BfArM concentrates on important and contemporary research focal points with regard to the marketing authorisation of medicinal products and improving the safety thereof as well as concerning the recording and assessment of risks in connection with medical devices.
  id: data-bfarm
  name: Research Data Centre at the BfArM
  url: https://www.bfarm.de/EN/BfArM/Tasks/Research/_node.html
- description: Tool that provides the user with an overview of available health data in Denmark and the entire application process, from initial idea to final application.
  id: danish-gateway
  name: Danish Research Health Data Gateway
  url: https://www.enindgangtilsundhedsdata.dk/en
- description: Tool to discover the Data held by the Irish Public Service
  id: irish-catalogue
  name: The Public Service Data Catalogue
  url: https://datacatalogue.gov.ie/
- description: Tool to find health data in the metadata catalogue in Portugal.
  id: portugal-catalogue
  name: The National health service metadata catalogue
  url: https://transparencia.sns.gov.pt/explore/?sort=modified
- description: Findata is the data permit authority for the social and health care sector in Finland.
  id: findata
  name: Findata
  url: https://findata.fi/en/
- description: French Health Data Hub that guarantees easy and unified, transparent and secure access to health data to improve the quality of care and patient support.
  id: french-hub
  name: French Health Data Hub
  url: https://www.health-data-hub.fr/
- description: HDR UK is a national institute with the aim to unite the UK’s health and care data to enable discoveries that improve people’s lives. We do this by uniting, improving and using health and care data as one national institute.
  id: hdr-uk
  name: Health Research Data UK
  url: https://www.hdruk.ac.uk/
- description: DAGitty is a browser-based environment for creating, editing, and analyzing causal diagrams (also known as directed acyclic graphs or causal Bayesian networks).
  id: dagitty
  name: DAGitty
  registry:
    biotools: dagitty
    fairsharing: dagitty
  url: https://www.dagitty.net/
- description: Quarto is an open-source scientific and technical publishing system that enables the creation of dynamic and reproducible content.
  id: quarto
  name: Quarto
  registry:
    tess: Quarto
  url: https://quarto.org/
- description: Bcftools is a set of tools for working with variant calls in the VCF format.
  id: bcftools
  name: Bcftools
  registry:
    biotools: bcftools
  url: https://samtools.github.io/bcftools/bcftools.html
- description: Qualimap is a quality control tool that assesses the quality of the sequencing data at different stages of the analysis pipeline, including read mapping, coverage, and expression analysis.
  id: qualimap
  name: Qualimap
  registry:
    biotools: qualimap
  url: http://qualimap.conesalab.org/
- description: GATK is a widely used tool for variant calling and genotyping from NGS data.
  id: gatk
  name: Genome Analysis Toolkit (GATK)
  registry:
    biotools: gatk
  url: https://gatk.broadinstitute.org/hc/en-us
- description: Picard is a suite of tools that provides quality control and processing of NGS data, including duplicate read removal, format conversion, and alignment.
  id: picard
  name: Picard
  registry:
    biotools: picard_tools
  url: https://broadinstitute.github.io/picard/
- description: Trimmomatic is a tool used for the removal of adapter sequences, low-quality reads, and sequences with ambiguous bases from NGS data.
  id: trimmomatic
  name: Trimmomatic
  registry:
    biotools: trimmomatic
    tess: Trimmomatic
  url: http://www.usadellab.org/cms/?page=trimmomatic
- description: FastQ Screen is a quality control tool used to detect contamination in sequencing data (FASTQ files).
  id: fastqc-screen
  name: FastQC Screen
  url: https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/
- description: GRAF pop is a software tool that infers the subject ancestry.
  id: graf-pop
  name: GRAF pop
  url: https://pubmed.ncbi.nlm.nih.gov/31151998/
- description: Tool that determines subject sexes using the genotypes.
  id: graf-sex
  name: GRAF sex
  url: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/GRAF_README.html
- description: Python data visualization library that provides a high-level interface for drawing attractive and informative statistical graphics.
  id: seaborn
  name: seaborn
  registry:
    tess: seaborn
  url: https://seaborn.pydata.org/
- description: Free software environment for statistical computing and graphics.
  id: r
  name: R
  registry:
    biotools: r
    tess: R
  url: https://www.r-project.org/
- description: Open source data analysis and manipulation tool, built on top of the Python programming language.
  id: pandas
  name: pandas
  registry:
    biotools: pandas
    tess: pandas
  url: https://pandas.pydata.org/
- description: Python library for scientific computing.
  id: numpy
  name: NumPy
  registry:
    biotools: numpy
    tess: NumPy
  url: https://numpy.org/
- description: Machine learning tools in Python
  id: scikit-learn
  name: Scikit-learn
  registry:
    biotools: scikit-learn
    tess: Scikit-learn
  url: https://scikit-learn.org/stable/
- description: Python library that uses machine learning to perform fuzzy matching, deduplication, and entity resolution quickly on structured data.
  id: dedupe
  name: dedupe
  url: https://github.com/dedupeio/dedupe
- description: Command line application to submit assemblies and transcriptomes to ENA.
  id: webin-cli
  name: Webin-CLI
  registry:
    tess: Webin-CLI
  url: https://github.com/enasequence/webin-cli
- description: Interface to query on the EGA data through Beacon v2
  id: ega-beacon
  name: EGA Beacon
  url: https://beacon.ega-archive.org/
- description: Beacon from UNottingham to query a backend OMOP database of synthetic COVID-19 patient EHRs (electronic health records).
  id: unott-beacon
  name: UNottingham Beacon
  url: https://beacon.nottingham.ac.uk
- description: The Bento platform enables the research community to explore the BQC19 cohort aggregate data.
  id: bento-platform
  name: Bento platform
  url: https://bqc19.bento.sd4h.ca/#/en/
- description: SARS-CoV-2 whole genome sequencing circuit of Andalusia
  id: andalusia-beacon
  name: SARS-COV-2 outbreak in Andalucia
  url: https://nextstrain.clinbioinfosspa.es/SARS-COV-2-latest
- description: The COVID-19 Beacon is a searchable platform for SARS-CoV-2 genomic variants conforming to the Beacon specifications of the Global Alliance for Genomics and Health but adjusted for viral genome searches.
  id: covid19-beacon
  name: COVID-19 BEACON
  url: https://d2eqg84un4jpac.cloudfront.net/
- description: A global network for genomic surveillance and infectious disease research
  id: viral-ai
  name: Viral AI
  url: https://viral.ai/collections
- description: EMBL-EBI's web portal for finding ontologies
  id: ols
  name: Ontology Lookup Service
  registry:
    biotools: ols
    fairsharing: Mkl9RR
    tess: Ontology Lookup Service
  url: https://www.ebi.ac.uk/ols/index
- description: A comprehensive repository of biomedical ontologies
  id: bioportal
  name: BioPortal
  registry:
    biotools: bioportal
    fairsharing: 4m97ah
    tess: BioPortal
  url: https://bioportal.bioontology.org
- description: Collaborative effort to develob interoperable ontologies for the biological sciences
  id: the-open-biological-and-biomedical-ontology-foundry
  name: The Open Biological and Biomedical Ontology (OBO) Foundry
  registry:
    fairsharing-coll: bsg-d001083
  url: http://obofoundry.org