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ASVmaker: A New Tool to Improve Taxonomic Identifications for Amplicon Sequencing Data

The taxonomic assignment of sequences obtained by high throughput amplicon sequencing poses a limitation for various applications in the biomedical, environmental, and agricultural fields. Identifications are constrained by the length of the obtained sequences and the computational processes employe...

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Autores principales: Plessis, Clément, Jeanne, Thomas, Dionne, Antoine, Vivancos, Julien, Droit, Arnaud, Hogue, Richard
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10647208/
https://www.ncbi.nlm.nih.gov/pubmed/37960035
http://dx.doi.org/10.3390/plants12213678
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author Plessis, Clément
Jeanne, Thomas
Dionne, Antoine
Vivancos, Julien
Droit, Arnaud
Hogue, Richard
author_facet Plessis, Clément
Jeanne, Thomas
Dionne, Antoine
Vivancos, Julien
Droit, Arnaud
Hogue, Richard
author_sort Plessis, Clément
collection PubMed
description The taxonomic assignment of sequences obtained by high throughput amplicon sequencing poses a limitation for various applications in the biomedical, environmental, and agricultural fields. Identifications are constrained by the length of the obtained sequences and the computational processes employed to efficiently assign taxonomy. Arriving at a consensus is often preferable to uncertain identification for ecological purposes. To address this issue, a new tool called “ASVmaker” has been developed to facilitate the creation of custom databases, thereby enhancing the precision of specific identifications. ASVmaker is specifically designed to generate reference databases for allocating amplicon sequencing data. It uses publicly available reference data and generates specific sequences derived from the primers used to create amplicon sequencing libraries. This versatile tool can complete taxonomic assignments performed with pre-trained classifiers from the SILVA and UNITE databases. Moreover, it enables the generation of comprehensive reference databases for specific genes in cases where no directly applicable database exists for taxonomic classification tools.
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spelling pubmed-106472082023-10-25 ASVmaker: A New Tool to Improve Taxonomic Identifications for Amplicon Sequencing Data Plessis, Clément Jeanne, Thomas Dionne, Antoine Vivancos, Julien Droit, Arnaud Hogue, Richard Plants (Basel) Article The taxonomic assignment of sequences obtained by high throughput amplicon sequencing poses a limitation for various applications in the biomedical, environmental, and agricultural fields. Identifications are constrained by the length of the obtained sequences and the computational processes employed to efficiently assign taxonomy. Arriving at a consensus is often preferable to uncertain identification for ecological purposes. To address this issue, a new tool called “ASVmaker” has been developed to facilitate the creation of custom databases, thereby enhancing the precision of specific identifications. ASVmaker is specifically designed to generate reference databases for allocating amplicon sequencing data. It uses publicly available reference data and generates specific sequences derived from the primers used to create amplicon sequencing libraries. This versatile tool can complete taxonomic assignments performed with pre-trained classifiers from the SILVA and UNITE databases. Moreover, it enables the generation of comprehensive reference databases for specific genes in cases where no directly applicable database exists for taxonomic classification tools. MDPI 2023-10-25 /pmc/articles/PMC10647208/ /pubmed/37960035 http://dx.doi.org/10.3390/plants12213678 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Plessis, Clément
Jeanne, Thomas
Dionne, Antoine
Vivancos, Julien
Droit, Arnaud
Hogue, Richard
ASVmaker: A New Tool to Improve Taxonomic Identifications for Amplicon Sequencing Data
title ASVmaker: A New Tool to Improve Taxonomic Identifications for Amplicon Sequencing Data
title_full ASVmaker: A New Tool to Improve Taxonomic Identifications for Amplicon Sequencing Data
title_fullStr ASVmaker: A New Tool to Improve Taxonomic Identifications for Amplicon Sequencing Data
title_full_unstemmed ASVmaker: A New Tool to Improve Taxonomic Identifications for Amplicon Sequencing Data
title_short ASVmaker: A New Tool to Improve Taxonomic Identifications for Amplicon Sequencing Data
title_sort asvmaker: a new tool to improve taxonomic identifications for amplicon sequencing data
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10647208/
https://www.ncbi.nlm.nih.gov/pubmed/37960035
http://dx.doi.org/10.3390/plants12213678
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