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Article Dans Une Revue Bioinformatics Année : 2016

RADIS: analysis of RAD-seq data for interspecific phylogeny

Résumé

In an attempt to make the processing of RAD-seq data easier and allow rapid and automated exploration of parameters/data for phylogenetic inference, we introduce the perl pipeline RADIS. Users of RADIS can let their raw Illumina data be processed up to phylogenetic tree inference, or stop (and restart) the process at some point. Different values for key parameters can be explored in a single analysis (e.g. loci building, sample/loci selection), making possible a thorough exploration of data. RADIS relies on Stacks for demultiplexing of data, removing PCR duplicates and building individual and catalog loci. Scripts have been specifically written for trimming of reads and loci/sample selection. Finally, RAxML is used for phylogenetic inferences, though other software may be utilized.
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Dates et versions

hal-01594524 , version 1 (26-09-2017)

Identifiants

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Astrid Cruaud, Mathieu Gautier, Jean-Pierre Rossi, Jean Yves Rasplus, Jerome Gouzy. RADIS: analysis of RAD-seq data for interspecific phylogeny. Bioinformatics, 2016, 32 (19), pp.3027-3028. ⟨10.1093/bioinformatics/btw352⟩. ⟨hal-01594524⟩
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