Quality checking and Demultiplexing

The quality of the reads was checked using FastQC. To summarize all the FastQC reports, the tool MultiQC (Ewels et al., 2016) created a single report to visualize the output. After quality checking, demultiplexing and SNP calling were performed using a script with specific parameters on the software Stacks v. 2.62 (Catchen et al., 2013). Demultiplexing raw reads with process_radtags tool allowed to: demultiplex; remove adapter sequences and the remainder of the restriction sites; correct or remove sequences with ambiguous barcodes and filter out reads with a raw Phred score of less than 10.