README: STACKS_and_QCfilter Author : Laura Gervais - Maria Bernard We provide FASTQ data (already demultiplexed and preprocessed) are available on the NCBI Sequence Read Archive with the accession number PRJNA533008. Those samples allows to run denovo_map.pl program of Stacks software. This folder contains : *full_indiv_barcorde.txt(not necessary for denovo_map.pl): A file with describing individuals in 4 columns. First column is to identify individuals with a unique integer ID. Second column is the name of the sequenced individuals. Individual names must be unique. Third column is the run name. Fourth column is the barcode sequence that allow to identify individuals in the run. *population.map: A file containing two columns with assignments of each of the samples to a particular population. Here all the individuals belong to the same population (population_index=1). First column indicates individual names (identical to full_indiv_barcode.txt). Second column is the population index. *stacksoutput_maxloc.vcf: Output file of *populations* program of Stacks software, run using the S1 MaxLoci set of parameters: -m=2 -M=2 -N=4 --max_locus_stacks=5 -n=1 *stacksoutput_minerr.vcf: Output file of *populations* program of Stacks software, run using the S2 MinError set of parameters: -m=11 -M=2 -N=4 --max_locus_stacks=5 -n=1 *stacksoutput_default.vcf: Output file of *populations* program of Stacks software, run using the S4 Default set of parameters: -m=3 -M=2 -N=4 --max_locus_stacks=3 -n=1 *stacksoutput_intermediate.vcf: Output file of *populations* program of Stacks software, run using the S3 Intermediate set of parameters: -m=7 -M=2 -N=4 --max_locus_stacks=5 -n=1 *indiv_to_rm.txt: Empty text file to fill with individual names needed to be remove for future analysis(e.g. individuals with too many missing data, replicate samples). *script_QCfiltering.sh: A shell script with explanations to run the different quality filtering procedures using VCF file as input. Please open it with Notepad.