title: obitools: a unix-inspired software package for DNA metabarcoding.
abstract: DNA metabarcoding offers new perspectives in biodiversity research. This recently developed approach to ecosystem study relies heavily on the use of next-generation sequencing (NGS) and thus calls upon the ability to deal with huge sequence data sets. The obitools package satisfies this requirement thanks to a set of programs specifically designed for analysing NGS data in a DNA metabarcoding context. Their capacity to filter and edit sequences while taking into account taxonomic annotation helps to set up tailor-made analysis pipelines for a broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses. The obitools package is distributed as an open source software available on the following website: http://metabarcoding.org/obitools. A Galaxy wrapper is available on the GenOuest core facility toolshed: http://toolshed.genouest.org.
authors.affiliation: Laboratoire d'Écologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourrier, BP 53, 38041, Grenoble Cedex-9, France.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Boyer
authors.affiliation: Laboratoire d'Écologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourrier, BP 53, 38041, Grenoble Cedex-9, France.
authors.forename: Céline
authors.initials: C
authors.lastname: Mercier
authors.affiliation: Laboratoire d'Écologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourrier, BP 53, 38041, Grenoble Cedex-9, France.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Bonin
authors.affiliation: GenOuest Core Facility, CNRS UMR 6074 IRISA-INRIA, Campus de Beaulieu, 35042, Rennes Cedex, France.
authors.forename: Yvan
authors.initials: Y
authors.lastname: Le Bras
authors.affiliation: Laboratoire d'Écologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourrier, BP 53, 38041, Grenoble Cedex-9, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Taberlet
authors.affiliation: Laboratoire d'Écologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourrier, BP 53, 38041, Grenoble Cedex-9, France.
authors.forename: Eric
authors.identifier: http://orcid.org/0000-0001-7507-6729
authors.initials: E
authors.lastname: Coissac
mesh_terms: D004247:DNA / Q000235:genetics*; D058893:DNA Barcoding, Taxonomic; D059014:High-Throughput Nucleotide Sequencing; D020407:Internet; D012984:Software
chemical_list: D004247:DNA
keywords: PCR errors; biodiversity; next-generation sequencing; sequence analysis; taxonomic annotation