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Mol Ecol Resour. 2016 Jan;16(1):176-82. doi: 10.1111/1755-0998.12428. Epub 2015 May 26.

obitools: a unix-inspired software package for DNA metabarcoding.

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Laboratoire d'Écologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourrier, BP 53, 38041, Grenoble Cedex-9, France.
GenOuest Core Facility, CNRS UMR 6074 IRISA-INRIA, Campus de Beaulieu, 35042, Rennes Cedex, France.


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: A Galaxy wrapper is available on the GenOuest core facility toolshed:


PCR errors; biodiversity; next-generation sequencing; sequence analysis; taxonomic annotation

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