Workshop 12: Marker development - pseudogene/aquaexcel GitHub Wiki
The overall RAD methodology:
(c) The Stacks pipeline
Check Stacks manual to learn more in detail of how to analyze metagenomics data.
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mkdir -p denovo
denovo_map.pl -M 3 -n 2 -T 2 --samples ./samples --popmap tutorial.pop.txt -o ./denovo
populations -P ./denovo -M tutorial.pop.txt -p 1 -r 0.50 -R 0.50 -t 2 --min_maf 0.01 --write_single_snp --plink --vcf --genepop
Check Github radmap