MAPtools: command-line tools for mappingby-sequencing and QTL-Seq analysis and visualization

Abstract Background Classical mutagenesis is a powerful tool that has allowed researchers to elucidate the molecular and genetic basis of a plethora of processes in many model species. The integration of these methods with modern massively parallel sequencing techniques, initially in model species b...

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Detalles Bibliográficos
Autores: Martínez-Guardiola, César, Parreño-Montoro, Ricardo, Candela, Héctor
Tipo de recurso: artículo
Fecha de publicación:2024
País:España
Institución:Universidad Miguel Hernández de Elche
Repositorio:REDIUMH. Depósito Digital de la UMH
OAI Identifier:oai:dspace.umh.es:11000/35313
Acceso en línea:https://hdl.handle.net/11000/35313
Access Level:acceso abierto
Palabra clave:CDU::5 - Ciencias puras y naturales::57 - Biología
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spelling MAPtools: command-line tools for mappingby-sequencing and QTL-Seq analysis and visualizationMartínez-Guardiola, CésarParreño-Montoro, RicardoCandela, HéctorCDU::5 - Ciencias puras y naturales::57 - BiologíaAbstract Background Classical mutagenesis is a powerful tool that has allowed researchers to elucidate the molecular and genetic basis of a plethora of processes in many model species. The integration of these methods with modern massively parallel sequencing techniques, initially in model species but currently also in many crop species, is accelerating the identification of genes underlying a wide range of traits of agronomic interest. Results We have developed MAPtools, an open-source Python3 application designed specifically for the analysis of genomic data from bulked segregant analysis experiments, including mapping-by-sequencing (MBS) and quantitative trait locus sequencing (QTL-seq) experiments. We have extensively tested MAPtools using datasets published in recent literature. Conclusions MAPtools gives users the flexibility to customize their bioinformatics pipeline with various commands for calculating allele count-based statistics, generating plots to pinpoint candidate regions, and annotating the effects of SNP and indel mutations. While extensively tested with plants, the program is versatile and applicable to any species for which a mapping population can be generated and a sequenced genome is available. Availability and implementation MAPtools is available under GPL v3.0 license and documented as a Python3 package at https://github.com/hcandela/MAPtools.BioMed CentralDepartamentos de la UMH::Biología Aplicada202520252024info:eu-repo/semantics/articleapplication/pdf13application/pdfhttps://hdl.handle.net/11000/35313reponame:REDIUMH. Depósito Digital de la UMHinstname:Universidad Miguel Hernández de ElcheIngléshttps://doi.org/10.1186/s13007-024-01222-2info:eu-repo/semantics/openAccessAttribution-NonCommercial-NoDerivatives 4.0 Internacionalhttp://creativecommons.org/licenses/by-nc-nd/4.0/oai:dspace.umh.es:11000/353132026-05-27T13:36:21Z
dc.title.none.fl_str_mv MAPtools: command-line tools for mappingby-sequencing and QTL-Seq analysis and visualization
title MAPtools: command-line tools for mappingby-sequencing and QTL-Seq analysis and visualization
spellingShingle MAPtools: command-line tools for mappingby-sequencing and QTL-Seq analysis and visualization
Martínez-Guardiola, César
CDU::5 - Ciencias puras y naturales::57 - Biología
title_short MAPtools: command-line tools for mappingby-sequencing and QTL-Seq analysis and visualization
title_full MAPtools: command-line tools for mappingby-sequencing and QTL-Seq analysis and visualization
title_fullStr MAPtools: command-line tools for mappingby-sequencing and QTL-Seq analysis and visualization
title_full_unstemmed MAPtools: command-line tools for mappingby-sequencing and QTL-Seq analysis and visualization
title_sort MAPtools: command-line tools for mappingby-sequencing and QTL-Seq analysis and visualization
dc.creator.none.fl_str_mv Martínez-Guardiola, César
Parreño-Montoro, Ricardo
Candela, Héctor
author Martínez-Guardiola, César
author_facet Martínez-Guardiola, César
Parreño-Montoro, Ricardo
Candela, Héctor
author_role author
author2 Parreño-Montoro, Ricardo
Candela, Héctor
author2_role author
author
dc.contributor.none.fl_str_mv Departamentos de la UMH::Biología Aplicada
dc.subject.none.fl_str_mv CDU::5 - Ciencias puras y naturales::57 - Biología
topic CDU::5 - Ciencias puras y naturales::57 - Biología
description Abstract Background Classical mutagenesis is a powerful tool that has allowed researchers to elucidate the molecular and genetic basis of a plethora of processes in many model species. The integration of these methods with modern massively parallel sequencing techniques, initially in model species but currently also in many crop species, is accelerating the identification of genes underlying a wide range of traits of agronomic interest. Results We have developed MAPtools, an open-source Python3 application designed specifically for the analysis of genomic data from bulked segregant analysis experiments, including mapping-by-sequencing (MBS) and quantitative trait locus sequencing (QTL-seq) experiments. We have extensively tested MAPtools using datasets published in recent literature. Conclusions MAPtools gives users the flexibility to customize their bioinformatics pipeline with various commands for calculating allele count-based statistics, generating plots to pinpoint candidate regions, and annotating the effects of SNP and indel mutations. While extensively tested with plants, the program is versatile and applicable to any species for which a mapping population can be generated and a sequenced genome is available. Availability and implementation MAPtools is available under GPL v3.0 license and documented as a Python3 package at https://github.com/hcandela/MAPtools.
publishDate 2024
dc.date.none.fl_str_mv 2024
2025
2025
dc.type.none.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://hdl.handle.net/11000/35313
url https://hdl.handle.net/11000/35313
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv https://doi.org/10.1186/s13007-024-01222-2
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
Attribution-NonCommercial-NoDerivatives 4.0 Internacional
http://creativecommons.org/licenses/by-nc-nd/4.0/
eu_rights_str_mv openAccess
rights_invalid_str_mv Attribution-NonCommercial-NoDerivatives 4.0 Internacional
http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.format.none.fl_str_mv application/pdf
13
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:REDIUMH. Depósito Digital de la UMH
instname:Universidad Miguel Hernández de Elche
instname_str Universidad Miguel Hernández de Elche
reponame_str REDIUMH. Depósito Digital de la UMH
collection REDIUMH. Depósito Digital de la UMH
repository.name.fl_str_mv
repository.mail.fl_str_mv
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