Bioinformatic scripts allowing the comparison of fungal metabarcoding pipelines

DOI

This dataset contains scripts and code that can be used to compare metabarcoding pipelines using a fungal mock community. These bioinformatics scripts were applied to the sequences available at https://doi.org/10.15454/8CVWRR (Pauvert et al. Bioinformatics matters: the accuracy of plant and soil community data is highly dependent on the metabarcoding pipeline. Submitted). They can be used to compare the performance of 360 software and parameter combinations. They are based on several softwares, including USEARCH (Edgar 2010), VSEARCH (Rognes et al. 2016) and DADA2 (Callahan et al. 2016). The code corresponds mainly to bash scripts and R files. README files are provided for clarity.

Identifier
DOI https://doi.org/10.15454/VKTWKR
Metadata Access https://entrepot.recherche.data.gouv.fr/oai?verb=GetRecord&metadataPrefix=oai_datacite&identifier=doi:10.15454/VKTWKR
Provenance
Creator Pauvert, Charlie; Buee, Marc; Laval, Valérie; Edel-Hermann, Véronique; Fauchery, Laure; Gautier, Angélique; Lesur Kupin, Isabelle; Vallance, Jessica; Vacher, Corinne
Publisher Recherche Data Gouv
Contributor Pauvert, Charlie; Vacher, Corinne
Publication Year 2018
Rights etalab 2.0; info:eu-repo/semantics/openAccess; https://spdx.org/licenses/etalab-2.0.html
OpenAccess true
Contact Pauvert, Charlie (INRA - Institut National de la Recherche Agronomique); Vacher, Corinne (Vacher, Corinne)
Representation
Resource Type Dataset
Format text/plain; charset=US-ASCII; application/gzip
Size 1288; 9261579
Version 4.0
Discipline Computer Science; Life Sciences; Basic Biological and Medical Research; Biology; Computer Science, Electrical and System Engineering; Engineering Sciences; Medicine; Omics; Microbial Ecology and Applied Microbiology