This file contains the metabarcoding pipeline and the reference databases used in the paper:
"Metabarcoding on planktonic larval stages: an efficient approach for detecting and investigating life cycle dynamics of benthic aliens"
Authors: M. Couton, T. Comtet, S. Le Cam, E. Corre, and F. Viard
Published in Management of Biological Invasions (in press; 2019)


Information contact : mcouton@sb-roscoff.fr
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The pipeline used is summarized in the Snakefile. 
It can be executed directly from a prompt command line on any data providing some modifications on the config file (config_metabarcoding).
All parameters for the different steps can be modified via the config file.
The parameters used to obtain the paper's results are described in the config file.

OBITools v1.2.11 and BLAST need to be installed before using the snakefile
All the other required scripts are available in this folder: 
	- taxo_file.csv is a table with species names associated with their accepted version according to WoRMS (last check Dec-2018)
	- Tableau_info_seq.py is a python script extracting information about each sequence from a fasta file and writing a table which will be used in the R script for taxonomical assignment.
	- Assign_Metab.R is a R script used to sort and analyse the results from blast

The custom reference databases (for COI and 18S) used for taxonomical assignment are available in blastdb format to be used by the snakefile. Note that the fasta format is available in the same DRYAD reporsitory.
All references gathered from GenBank, BOLD, SILVA or PR2 are associated with their Accession number (or equivalent for other public databases): argument "AccNum" in the header of the sequence
For sequences produced locally, the voucher code was included in the header of the sequence (argument "code")
