Barnabé Christian, Sempere Marie-Elyse, Manzanilla Vincent, Moo-Millan Joel, Amblard-Rambert Antoine, Waleckx Etienne. 2024. mbctools: A user-friendly metabarcoding and cross-platform pipeline for analyzing multiple amplicon sequencing data across a large diversity of organisms. Peer Community Journal, 4:e114, 13 p.
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Url - autres données associées : https://github.com/GuilhemSempere/mbctools / Url - autres données associées : https://pypi.org/project/mbctools/
Résumé : We developed a python package called mbctools, designed to offer a cross-platform tool for processing amplicon data from various organisms in the context of metabarcoding studies. It can handle the most common tasks in metabarcoding pipelines such as paired-end merging, primer trimming, quality filtering, sequence denoising, zero-radius operational taxonomic unit (ZOTU) filtering, and has the capability to process multiple genetic markers simultaneously. mbc- tools is a menu-driven program that eliminates the need for expertise in command-line skills and ensures documentation of each analysis for reproducibility purposes. The software, de- signed to run in a console, offers an interactive experience, guided by keyboard inputs, assisting users along the way through data processing and hiding the complexity of command lines by letting them concentrate on selecting parameters to apply in each step of the process. In our workflow, VSEARCH is utilized for processing fastq files derived from amplicon- based Next-Generation Sequencing data. This software is a versatile open-source tool for pro- cessing amplicon sequences, offering advantages such as high speed, efficient memory usage, and the ability to handle large datasets. It provides functions for various tasks such as dereplication, clustering, chimera detection, and taxonomic assignment. VSEARCH is thus very effi- cient in retrieving the overall diversity of a sample. To adapt to the diversity of projects in metabarcoding, we facilitate the reprocessing of datasets with the possibility to adjust pa- rameters. mbctools can also be launched in a headless mode, making it suited for integration into pipelines running on High-Performance Computing environments.
Mots-clés Agrovoc : marqueur génétique, phylogénie, traitement des données, logiciel, Trypanosoma, variation génétique, analyse de données
Mots-clés géographiques Agrovoc : Mexique
Mots-clés libres : Metabarcoding, Software, Pipeline
Agences de financement hors UE : Consejo Nacional de Ciencia y Tecnología, Institut de Recherche pour le Développement
Auteurs et affiliations
- Barnabé Christian, IRD (FRA)
- Sempere Marie-Elyse, CIRAD-PERSYST-UMR Qualisud (FRA) - auteur correspondant
- Manzanilla Vincent, IRD (FRA) - auteur correspondant
- Moo-Millan Joel, UADY (MEX)
- Amblard-Rambert Antoine, IRD (FRA)
- Waleckx Etienne, IRD (FRA) - auteur correspondant
Source : Cirad-Agritrop (https://agritrop.cirad.fr/611315/)
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