Contains scripts and part of the output data of running *Stacks* with the demultiplexed-lane-effect-corrected data (see section **Demultiplexing and dropbase/0.1DropBase** of this repository) available at the Sequence Read Archive (SRA), accession SRP035472; to subsequently produce SNP (*.SNP) and coverage (*.COV) tsv matrices and to run the *populations* program of Stacks with the selected loci of the downstream analyses. The Stacks parameter values corresponds to the experiments defined as *1) Exploratory analysis of Stacks assembly key parameters and SNP calling model using replicates* and *2) Effect of using different parameters on the output information content and on the detection of genetic structuring
