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.