DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets

DNA metabarcoding is broadly used in biodiversity studies encompassing a wide range of organisms. Erroneous amplicons, generated during amplification and sequencing procedures, constitute one of the major sources of concern for the interpretation of metabarcoding results. Several denoising programs...

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Detalles Bibliográficos
Autores: Antich, Adrià, Palacín Cabañas, Cruz, Turon Barrera, Xavier, Wangensteen Fuentes, Owen S. (Simon)
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2022
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:2445/191218
Acceso en línea:https://hdl.handle.net/2445/191218
Access Level:acceso abierto
Palabra clave:ADN
Entropia (Teoria de la informació)
DNA
Entropy (Information theory)
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spelling DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasetsAntich, AdriàPalacín Cabañas, CruzTuron Barrera, XavierWangensteen Fuentes, Owen S. (Simon)ADNEntropia (Teoria de la informació)DNAEntropy (Information theory)DNA metabarcoding is broadly used in biodiversity studies encompassing a wide range of organisms. Erroneous amplicons, generated during amplification and sequencing procedures, constitute one of the major sources of concern for the interpretation of metabarcoding results. Several denoising programs have been implemented to detect and eliminate these errors. However, almost all denoising software currently available has been designed to process non-coding ribosomal sequences, most notably prokaryotic 16S rDNA. The growing number of metabarcoding studies using coding markers such as COI or RuBisCO demands a re-assessment and calibration of denoising algorithms. Here we present DnoisE, the first denoising program designed to detect erroneous reads and merge them with the correct ones using information from the natural variability (entropy) associated to each codon position in coding barcodes. We have developed an open-source software using a modified version of the UNOISE algorithm. DnoisE implements different merging procedures as options, and can incorporate codon entropy information either retrieved from the data or supplied by the user. In addition, the algorithm of DnoisE is parallelizable, greatly reducing runtimes on computer clusters. Our program also allows different input file formats, so it can be readily incorporated into existing metabarcoding pipelines.PeerJ2022202220222022info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersion16 p.application/pdfhttps://hdl.handle.net/2445/191218Articles publicats en revistes (Biologia Evolutiva, Ecologia i Ciències Ambientals)reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésReproducció del document publicat a: https://doi.org/10.7717/peerj.12758PeerJ, 2022, vol. 10, p. e12758https://doi.org/10.7717/peerj.12758cc-by (c) Antich, Adrià et al., 2022https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:2445/1912182026-05-29T05:05:01Z
dc.title.none.fl_str_mv DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets
title DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets
spellingShingle DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets
Antich, Adrià
ADN
Entropia (Teoria de la informació)
DNA
Entropy (Information theory)
title_short DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets
title_full DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets
title_fullStr DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets
title_full_unstemmed DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets
title_sort DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets
dc.creator.none.fl_str_mv Antich, Adrià
Palacín Cabañas, Cruz
Turon Barrera, Xavier
Wangensteen Fuentes, Owen S. (Simon)
author Antich, Adrià
author_facet Antich, Adrià
Palacín Cabañas, Cruz
Turon Barrera, Xavier
Wangensteen Fuentes, Owen S. (Simon)
author_role author
author2 Palacín Cabañas, Cruz
Turon Barrera, Xavier
Wangensteen Fuentes, Owen S. (Simon)
author2_role author
author
author
dc.subject.none.fl_str_mv ADN
Entropia (Teoria de la informació)
DNA
Entropy (Information theory)
topic ADN
Entropia (Teoria de la informació)
DNA
Entropy (Information theory)
description DNA metabarcoding is broadly used in biodiversity studies encompassing a wide range of organisms. Erroneous amplicons, generated during amplification and sequencing procedures, constitute one of the major sources of concern for the interpretation of metabarcoding results. Several denoising programs have been implemented to detect and eliminate these errors. However, almost all denoising software currently available has been designed to process non-coding ribosomal sequences, most notably prokaryotic 16S rDNA. The growing number of metabarcoding studies using coding markers such as COI or RuBisCO demands a re-assessment and calibration of denoising algorithms. Here we present DnoisE, the first denoising program designed to detect erroneous reads and merge them with the correct ones using information from the natural variability (entropy) associated to each codon position in coding barcodes. We have developed an open-source software using a modified version of the UNOISE algorithm. DnoisE implements different merging procedures as options, and can incorporate codon entropy information either retrieved from the data or supplied by the user. In addition, the algorithm of DnoisE is parallelizable, greatly reducing runtimes on computer clusters. Our program also allows different input file formats, so it can be readily incorporated into existing metabarcoding pipelines.
publishDate 2022
dc.date.none.fl_str_mv 2022
2022
2022
2022
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/191218
url https://hdl.handle.net/2445/191218
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Reproducció del document publicat a: https://doi.org/10.7717/peerj.12758
PeerJ, 2022, vol. 10, p. e12758
https://doi.org/10.7717/peerj.12758
dc.rights.none.fl_str_mv cc-by (c) Antich, Adrià et al., 2022
https://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv cc-by (c) Antich, Adrià et al., 2022
https://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 16 p.
application/pdf
dc.publisher.none.fl_str_mv PeerJ
publisher.none.fl_str_mv PeerJ
dc.source.none.fl_str_mv Articles publicats en revistes (Biologia Evolutiva, Ecologia i Ciències Ambientals)
reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,81155

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