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## Using this workflow
> **Benchmarking bioinformatic tools for fast and accurate eDNA metabarcoding species identification**
>
> *Laetitia Mathon, Alice Valentini, Pierre-Edouard Guerin, Eric Normandeau, Cyril Noel, Clément Lionnet, Emilie Boulanger, Wilfried Thuiller, Louis Bernatchez, David Mouillot, Tony Dejean, Stephanie Manel*
>
> Molecular Ecology Resources. 2021 May 18. DOI [10.1111/1755-0998.13430](https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13430)
> **Blind assessment of vertebrate taxonomic diversity across spatial scales by clustering environmental DNA metabarcoding sequences**
>
> *Virginie Marques, Pierre‐Edouard Guerin, Mathieu Rocle, Alice Valentini, Stephanie Manel, David Mouillot, Tony Dejean*
>
> Ecography. 2020 Aug 04. DOI: [10.1111/ecog.05049](https://onlinelibrary.wiley.com/doi/10.1111/ecog.05049)
## Barcodes
### Vert01 Riaz et al 2011
> **EcoPrimers: Inference of new DNA barcode markers from whole genome sequence analysis**
>
> *Riaz T, Shehzad W, Viari A, Pompanon F, Taberlet P, Coissac E.*
>
> Nucleic Acids Research. 2011 Nov. DOI: [10.1093/nar/gkr732](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3241669/)
### Chond01 Taberlet et al 2018 (book)
> **Environmental DNA: For Biodiversity Research and Monitoring**
>
> *Taberlet, P., Bonin, A., Zinger, L., and Coissac E.*
>
> New York, NY: Oxford University Press. DOI: [10.1093/oso/9780198767220.001.0001
](https://oxford.universitypressscholarship.com/view/10.1093/oso/9780198767220.001.0001/oso-9780198767220)
## Teleo01 Valentini et al 2016
> **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 R Møller, Eske Willerslev, Tony Dejean*
>
> Molecular Ecology. 2016 Feb. DOI: [10.1111/mec.13428](https://pubmed.ncbi.nlm.nih.gov/26479867/)
## Mamm01 Taaberlet et al 2018
> **Environmental DNA: For Biodiversity Research and Monitoring**
>
> *Taberlet, P., Bonin, A., Zinger, L., and Coissac E.*
>
> New York, NY: Oxford University Press. DOI: [10.1093/oso/9780198767220.001.0001
](https://oxford.universitypressscholarship.com/view/10.1093/oso/9780198767220.001.0001/oso-9780198767220)
# Dependencies
## SWARM2
> **Swarm v2: highly-scalable and high-resolution amplicon clustering**
>
> *Frédéric Mahé1, Torbjørn Rognes, Christopher Quince, Colomban de Vargas, Micah Dunthorn*
>
> PeerJ. 2015 Dec. 10. DOI: [10.7717/peerj.1420](https://doi.org/10.7717/peerj.1420)
## VSEARCH
> **VSEARCH: a versatile open source tool for metagenomics**
>
> *Torbjørn Rognes​, Tomáš Flouri, Ben Nichols, Christopher Quince, Frédéric Mahé*
>
> PeerJ. 2016 Oct. 18. DOI: [10.7717/peerj.2584](https://doi.org/10.7717/peerj.2584)
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