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metaGOflow: a workflow for the analysis of marine genomic observatories shotgun metagenomics data

2023Journal article Open access
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dc.contributor.authorZafeiropoulos, Haris
dc.contributor.authorBeracochea, Martin
dc.contributor.authorNinidakis, Stelios
dc.contributor.authorExter, Katrina
dc.contributor.authorPotirakis, Antonis
dc.contributor.authorDe Moro, Gianluca
dc.contributor.authorRichardson, Lorna
dc.contributor.authorCorre, Erwan
dc.contributor.authorMachado, João Paulo
dc.contributor.authorPafilis, Evangelos
dc.contributor.authorKotoulas, Georgios
dc.contributor.authorSanti, Ioulia
dc.contributor.authorFinn, Robert D
dc.contributor.authorJ. Cox, Cymon
dc.contributor.authorPavloudi, Christina
dc.date.accessioned2024-04-11T09:11:07Z
dc.date.available2024-04-11T09:11:07Z
dc.date.issued2023
dc.description.abstractBackground: Genomic Observatories (GOs) are sites of long-term scientific study that undertake regular assessments of the genomic biodiversity. The European Marine Omics Biodiversity Observation Network (EMO BON) is a network of GOs that conduct regular biological community samplings to generate environmental and metagenomic data of microbial communities from designated marine stations around Europe. The development of an effective workflow is essential for the analysis of the EMO BON metagenomic data in a timely and reproducible manner. Findings: Based on the established MGnify resource, we developed metaGOflow. meta GOflow supports the fast inference of taxonomic profiles from GO-derived data based on ribosomal RNA genes and their functional annotation using the raw reads. Thanks to the Research Object Crate packaging, relevant metadata about the sample under study, and the details of the bioinformatics analysis it has been subjected to, are inherited to the data product while its modular implementation allows running the workflow partially. The analysis of 2 EMO BON samples and 1 Tara Oceans sample was performed as a use case. Conclusions: metaGOflow is an efficient and robust workflow that scales to the needs of projects producing big metagenomic data such as EMO BON. It highlights how containerization technologies along with modern workflow languages and metadata package approaches can support the needs of researchers when dealing with ever-increasing volumes of biological data. Despite being initially oriented to address the needs of EMO BON, metaGOflowis a flexible and easy-to-use workflow that can be broadly used for one-sample-at-a-time analysis of shotgun metagenomics data.pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.doi10.1093/gigascience/giad078pt_PT
dc.identifier.issn2047-217X
dc.identifier.urihttp://hdl.handle.net/10400.1/20624
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherOxford University Presspt_PT
dc.relationProviding an open collaborative space for digital biology in Europe
dc.relationGENETIC AND MORPHOLOGICAL DIFFERENTIATION IN ESTUARINE ORGANISMS WITH CONTRASTING DISPERSAL MODES
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.subjectShotgun metagenomicspt_PT
dc.subjectMGnifypt_PT
dc.subjectCommon Workflow Language (CWL)pt_PT
dc.subjectContainerspt_PT
dc.subjectProvenancept_PT
dc.subjectRO-Cratept_PT
dc.titlemetaGOflow: a workflow for the analysis of marine genomic observatories shotgun metagenomics datapt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleProviding an open collaborative space for digital biology in Europe
oaire.awardTitleGENETIC AND MORPHOLOGICAL DIFFERENTIATION IN ESTUARINE ORGANISMS WITH CONTRASTING DISPERSAL MODES
oaire.awardURIinfo:eu-repo/grantAgreement/EC/H2020/824087/EU
oaire.awardURIinfo:eu-repo/grantAgreement/FCT//SFRH%2FBD%2F14325%2F2003/PT
oaire.citation.titleGigaSciencept_PT
oaire.citation.volume12pt_PT
oaire.fundingStreamH2020
person.familyNameDe Moro
person.familyNameMachado
person.familyNameCox
person.givenNameGianluca
person.givenNameJoão Paulo
person.givenNameCymon
person.identifier.ciencia-id2F1D-EF8E-A023
person.identifier.ciencia-idCE18-6E56-7947
person.identifier.ciencia-id6B15-9771-1D04
person.identifier.orcid0000-0002-5542-0278
person.identifier.orcid0000-0002-7404-9670
person.identifier.orcid0000-0002-4927-979X
person.identifier.ridD-1303-2012
person.identifier.scopus-author-id42461272200
person.identifier.scopus-author-id7402112716
project.funder.identifierhttp://doi.org/10.13039/501100008530
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameEuropean Commission
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
relation.isAuthorOfPublication2cc20acc-b859-4f8f-aea7-4b11df1ff0b1
relation.isAuthorOfPublicationbb4d7baf-a10b-4f8a-9b97-e5798931b981
relation.isAuthorOfPublication82c3689c-60b6-440d-9d7b-49e6dbd6861b
relation.isAuthorOfPublication.latestForDiscoverybb4d7baf-a10b-4f8a-9b97-e5798931b981
relation.isProjectOfPublication704a9d89-0efc-4595-90f9-412b1e3d8178
relation.isProjectOfPublicatione07573ca-7c1c-4b41-aef0-7277930ae6ea
relation.isProjectOfPublication.latestForDiscovery704a9d89-0efc-4595-90f9-412b1e3d8178

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