Journal ArticleDOI
obitools: a unix-inspired software package for DNA metabarcoding.
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The obitools package satisfies this requirement thanks to a set of programs specifically designed for analysing NGS data in a DNA metabarcoding context, helping to set up tailor‐made analysis pipelines for a broad range of DNA metabARCoding applications, including biodiversity surveys or diet analyses.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.read more
Citations
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Environmental DNA metabarcoding: transforming how we survey animal and plant communities
Kristy Deiner,Holly M. Bik,Elvira Mächler,Elvira Mächler,Mathew Seymour,Anaïs Lacoursière-Roussel,Florian Altermatt,Florian Altermatt,Simon Creer,Iliana Bista,Iliana Bista,David M. Lodge,Natasha de Vere,Michael E. Pfrender,Louis Bernatchez +14 more
TL;DR: The use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance are reviewed, which distill what is known about the ability of different eDNA sample types to approximate richness in space and across time.
Journal ArticleDOI
FROGS: Find, Rapidly, OTUs with Galaxy Solution.
Frédéric Escudié,Lucas Auer,Maria Bernard,Mahendra Mariadassou,Laurent Cauquil,Katia Vidal,Sarah Maman,Guillermina Hernandez-Raquet,Sylvie Combes,Géraldine Pascal +9 more
TL;DR: This Galaxy‐supported pipeline, called FROGS, is designed to analyze large sets of amplicon sequences and produce abundance tables of Operational Taxonomic Units (OTUs) and their taxonomic affiliation to highlight databases conflicts and uncertainties.
Data from: Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding
Alice Valentini,Pierre Taberlet,Claude Miaud,Raphaël Civade,Jelger Herder,Philip Francis Thomsen,Eva Bellemain,Aurélien Besnard,Eric Coissac,Frédéric Boyer,Coline Gaboriaud,Pauline Jean,Nicolas Poulet,Nicolas Roset,Gordon H. Copp,Philippe Geniez,Didier Pont,Christine Argillier,Jean-Marc Baudoin,Tiphaine Peroux,Alain J. Crivelli,Anthony Olivier,Manon Acqueberge,Matthieu Le Brun,Peter Möller,Eske Willerslev,Tony Dejean +26 more
TL;DR: It is argued that the proposed DNA‐based approach has the potential to become the next‐generation tool for ecological studies and standardized biodiversity monitoring in a wide range of aquatic ecosystems.
Journal ArticleDOI
Mycobiome diversity: high-throughput sequencing and identification of fungi.
R. Henrik Nilsson,Sten Anslan,Mohammad Bahram,Christian Wurzbacher,Petr Baldrian,Leho Tedersoo +5 more
TL;DR: An overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis are provided, and advice for leveraging next-generation technologies to explore mycobiome diversity in different habitats is provided.
Journal ArticleDOI
Environmental DNA from Seawater Samples Correlate with Trawl Catches of Subarctic, Deepwater Fishes.
Philip Francis Thomsen,Peter Rask Møller,Eva Egelyng Sigsgaard,Steen Wilhelm Knudsen,Ole A Jørgensen,Eske Willerslev,Eske Willerslev,Eske Willerslev +7 more
TL;DR: This study demonstrates that eDNA reads can be used as a qualitative and quantitative proxy for marine fish assemblages in deepwater oceanic habitats as well as to monitoring effects of ongoing climate change on marine biodiversity—especially in polar ecosystems.
References
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Journal ArticleDOI
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