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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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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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. |
format | Online Article Text |
id | pubmed-10647208 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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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