In an attempt to make easier and standardize the processing of
RAD-seq data for phylogenetic inference, while allowing fast and
automated exploration of key analytical options, we designed the
user friendly perl pipeline RADIS.
RADIS is designed to run on Linux and Unix platforms and freely
available from this website.
The processing of raw data has been split up into two steps: data
cleaning and data analysis.
Users can choose i) to let their raw Illumina data be processed up
to phylogenetic tree inference (RADIS.pl)
ii) to perform only data cleaning (RADIS_step1_data_cleaning.pl)
iii) to perform only data analysis (RADIS_step2_data_analysis.pl)
Last version of Stacks tested for compatibility : Stacks-1.32
Last version of RAxML tested for compatibility : RAxML-8.2.4
If you use RADIS, please cite external programs used by the
pipeline. Many thanks!
Suggested citation: "Analyses were performed using the Perl
(Cruaud et al., 2016) that relies on Stacks
(Catchen et al. 2011, 2013) for demultiplexing of data, removing
PCR duplicates and building individual and catalog loci and RAxML
(Statmatakis, 2006 a, b) for phylogenetic inferences".
Catchen J., Amores
A., Hohenlohe P., Cresko W., Postlethwait J. 2011. Stacks:
building and genotyping loci de novo from short-read
sequences. G3: Genes, Genomes, Genetics, 1 : 171-182.
Catchen J., Hohenlohe P.A., Bassham S., Amores A., Cresko
W.A. 2013. Stacks: an analysis tool set for population
Ecology, 22 : 3124-3140.
M.* (eq. contributors), Rossi
J. (submitted). RADIS: Analysis of RAD-seq data for
InterSpecific phylogeny. Bioinformatics
Stamatakis A. 2006a. Phylogenetic models of rate
heterogeneity: A High Performance Computing Perspective.
International Parallel and Distributed Processing Symposium
(IPDPS 2006), Rhodes Island, Greece, 8 pp.
Stamatakis A. 2006b. RAxML-VI-HPC: maximum likelihood-based
phylogenetic analyses with thousands of taxa and mixed
22 : 2688-2690.