SARS-CoV-2 survey of reads data and phylogenetic analysis of two datasets

[Description of methods used for collection/generation of data] A worldwide survey using the GISAID EpiCov database was conducted on 2022-06-15, resulting in the collection of a SARS-CoV-2 genome dataset (available via DOI: 10.55876/gis8.230801ex). Another worldwide survey using the ENA database was...

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Detalhes bibliográficos
Autores: Álvarez-Herrera, Miguel, Ruiz-Rodríguez, Paula, Navarro-Domínguez, Beatriz, Bracho, María Alma, González-Candelas, Fernando, Comas, Iñaki, Coscollá, Mireia
Tipo de documento: conjunto de datos
Data de publicação:2025
País:España
Recursos:Consejo Superior de Investigaciones Científicas (CSIC)
Repositório:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/378670
Acesso em linha:http://hdl.handle.net/10261/378670
https://doi.org/10.20350/digitalCSIC/17032
Access Level:Acceso aberto
Palavra-chave:SARS-CoV-2
Spike
Transmission
Snakemake
id ES_48673944dbf05165c350e2d2012edd5d
oai_identifier_str oai:digital.csic.es:10261/378670
network_acronym_str ES
network_name_str España
repository_id_str
dc.title.none.fl_str_mv SARS-CoV-2 survey of reads data and phylogenetic analysis of two datasets
title SARS-CoV-2 survey of reads data and phylogenetic analysis of two datasets
spellingShingle SARS-CoV-2 survey of reads data and phylogenetic analysis of two datasets
Álvarez-Herrera, Miguel
SARS-CoV-2
Spike
Transmission
Snakemake
title_short SARS-CoV-2 survey of reads data and phylogenetic analysis of two datasets
title_full SARS-CoV-2 survey of reads data and phylogenetic analysis of two datasets
title_fullStr SARS-CoV-2 survey of reads data and phylogenetic analysis of two datasets
title_full_unstemmed SARS-CoV-2 survey of reads data and phylogenetic analysis of two datasets
title_sort SARS-CoV-2 survey of reads data and phylogenetic analysis of two datasets
dc.creator.none.fl_str_mv Álvarez-Herrera, Miguel
Ruiz-Rodríguez, Paula
Navarro-Domínguez, Beatriz
Bracho, María Alma
González-Candelas, Fernando
Comas, Iñaki
Coscollá, Mireia
author Álvarez-Herrera, Miguel
author_facet Álvarez-Herrera, Miguel
Ruiz-Rodríguez, Paula
Navarro-Domínguez, Beatriz
Bracho, María Alma
González-Candelas, Fernando
Comas, Iñaki
Coscollá, Mireia
author_role author
author2 Ruiz-Rodríguez, Paula
Navarro-Domínguez, Beatriz
Bracho, María Alma
González-Candelas, Fernando
Comas, Iñaki
Coscollá, Mireia
author2_role author
author
author
author
author
author
dc.contributor.none.fl_str_mv European Commission
Generalitat Valenciana
Ministerio de Ciencia e Innovación (España)
Agencia Estatal de Investigación (España)
Álvarez-Herrera, Miguel [0000-0002-7922-3180]
Ruiz-Rodríguez, Paula [0000-0003-0727-5974]
Bracho, María Alma [0000-0002-9204-5526]
González-Candelas, Fernando [0000-0002-0879-5798]
Comas, Iñaki [0000-0001-5504-9408]
Coscollá, Mireia [0000-0003-0752-0538]
Álvarez-Herrera, Miguel [m.alvarez.herrera@csic.es]
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv SARS-CoV-2
Spike
Transmission
Snakemake
topic SARS-CoV-2
Spike
Transmission
Snakemake
description [Description of methods used for collection/generation of data] A worldwide survey using the GISAID EpiCov database was conducted on 2022-06-15, resulting in the collection of a SARS-CoV-2 genome dataset (available via DOI: 10.55876/gis8.230801ex). Another worldwide survey using the ENA database was conducted on 2024-12-10. The second survey returned raw reads, and so the code and main processed files are made available here. The "output" folder contains the pipeline output files, including lineage assignment and repaired deletion identification results. Then, transcluster v2.1.0 was run on these datasets. For each dataset, input files containing lists of sample identifiers are contained in the "input" folder. The "output" folder contains the pipeline output files, consisting on a separate folder for each of the input lists, as well as a "summary" folder. Each "config/config.yaml" file describes the pipeline configuration of each run.
publishDate 2025
dc.date.none.fl_str_mv 2025
2025
2025
dc.type.none.fl_str_mv info:eu-repo/semantics/dataset
http://purl.org/coar/resource_type/c_ddb1
format dataset
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/378670
https://doi.org/10.20350/digitalCSIC/17032
url http://hdl.handle.net/10261/378670
https://doi.org/10.20350/digitalCSIC/17032
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/AEI//CNS2022-135116
info:eu-repo/grantAgreement/AEI//CNS2022-135100
Álvarez-Herrera, Miguel; Ruiz-Rodríguez, Paula; Navarro-Domínguez, Beatriz; Zulaica, Joao; Grau, Brayan; Bracho, María Alma; Guerreiro, Manuel; Aguilar-Gallardo, Cristobal; González-Candelas, Fernando; Comas, Iñaki; Geller, Ron; Coscollá, Mireia. Genome data artifacts and functional studies of deletion repair in the BA.1 SARS-CoV-2 spike protein. https://doi.org/10.1093/ve/veaf015. https://doi.org/10.1093/ve/veaf015
Snakemake v8.25.3 was used originally. Conda environment definitions are provided for reproducibility.
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/vnd.ms-excel
dc.publisher.none.fl_str_mv DIGITAL.CSIC
publisher.none.fl_str_mv DIGITAL.CSIC
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869407357666066432
spelling SARS-CoV-2 survey of reads data and phylogenetic analysis of two datasetsÁlvarez-Herrera, MiguelRuiz-Rodríguez, PaulaNavarro-Domínguez, BeatrizBracho, María AlmaGonzález-Candelas, FernandoComas, IñakiCoscollá, MireiaSARS-CoV-2SpikeTransmissionSnakemake[Description of methods used for collection/generation of data] A worldwide survey using the GISAID EpiCov database was conducted on 2022-06-15, resulting in the collection of a SARS-CoV-2 genome dataset (available via DOI: 10.55876/gis8.230801ex). Another worldwide survey using the ENA database was conducted on 2024-12-10. The second survey returned raw reads, and so the code and main processed files are made available here. The "output" folder contains the pipeline output files, including lineage assignment and repaired deletion identification results. Then, transcluster v2.1.0 was run on these datasets. For each dataset, input files containing lists of sample identifiers are contained in the "input" folder. The "output" folder contains the pipeline output files, consisting on a separate folder for each of the input lists, as well as a "summary" folder. Each "config/config.yaml" file describes the pipeline configuration of each run.[Methods for processing the data] Each compressed tarball contain files that are inputs or outputs from self-contained Snakemake workflows with per-rule conda environments that can be easily replicated via a one-line command line command. Further pipeline documentation is available at https://github.com/PathoGenOmics-Lab/ena-spike-ntd-repdel-analysis and https://github.com/PathoGenOmics-Lab/transcluster.Processed data, code, configuration files and main results of a survey of raw reads data, and phylogenetic analyses of two datasets of SARS-CoV-2 records assigned to the BA.1 Omicron lineage carrying spike NTD deletion repairs. The survey brought out 1,541,892 matching records as of 10 December 2024, of which 464,859 records selected at random for further analysis. For each, FASTQ files were retrieved from via the ENA Portal API and processed to detect the specific genetic variants. For the phylogenetic analysis, aligned genomes were placed on a mutation-annotated tree, and clusters were detected using a breadth-first search approach. Additionally, a normalized clustering index was estimated for each cluster. This metric can be interpreted as an estimation of transmission fitness if observations are backed by reads data. Finally, a series of figures (including sample timelines, comparisons of estimated fitness and missing data) were generated. The pipeline used for this analysis, transcluster v2.1.0, is a Snakemake workflow released as free software under the GNU GPLv3 license. The source code is included here, and is also available in GitHub (survey: https://github.com/PathoGenOmics-Lab/ena-spike-ntd-repdel-analysis; phylogenetic analysis: https://github.com/PathoGenOmics-Lab/transcluster).PTI+Salud Global – European Commission – NextGenerationEU/ PRTR (Regulation EU 2020/2094), Generalitat Valenciana and the European Social Fund “ESF Investing in your future” (CIACIF/2022/333), MCIN/AEI/10.13039/501100011033 and the European Union NextGenerationEU/PRTR (CNS2022-135116 and CNS2022-135100).File List: ena-analysis.tar.xz, transcluster-ena.tar.xz, transcluster-gisaid.tar.xzPeer reviewedDIGITAL.CSICEuropean CommissionGeneralitat ValencianaMinisterio de Ciencia e Innovación (España)Agencia Estatal de Investigación (España)Álvarez-Herrera, Miguel [0000-0002-7922-3180]Ruiz-Rodríguez, Paula [0000-0003-0727-5974]Bracho, María Alma [0000-0002-9204-5526]González-Candelas, Fernando [0000-0002-0879-5798]Comas, Iñaki [0000-0001-5504-9408]Coscollá, Mireia [0000-0003-0752-0538]Álvarez-Herrera, Miguel [m.alvarez.herrera@csic.es]Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202520252025info:eu-repo/semantics/datasethttp://purl.org/coar/resource_type/c_ddb1application/vnd.ms-excelhttp://hdl.handle.net/10261/378670https://doi.org/10.20350/digitalCSIC/17032reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI//CNS2022-135116info:eu-repo/grantAgreement/AEI//CNS2022-135100Álvarez-Herrera, Miguel; Ruiz-Rodríguez, Paula; Navarro-Domínguez, Beatriz; Zulaica, Joao; Grau, Brayan; Bracho, María Alma; Guerreiro, Manuel; Aguilar-Gallardo, Cristobal; González-Candelas, Fernando; Comas, Iñaki; Geller, Ron; Coscollá, Mireia. Genome data artifacts and functional studies of deletion repair in the BA.1 SARS-CoV-2 spike protein. https://doi.org/10.1093/ve/veaf015. https://doi.org/10.1093/ve/veaf015Snakemake v8.25.3 was used originally. Conda environment definitions are provided for reproducibility.Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3786702026-05-22T06:33:51Z
score 15.811543

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