Stacks is a software pipeline for building loci out of a set of short-read sequenced samples. Stacks was developed for the purpose of building genetic maps from RAD-Tag Illumina sequence data, but can also be readily applied to population studies, and phylogeography.
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J. Catchen, A. Amores, P. Hohenlohe, W. Cresko, and J. Postlethwait.
Stacks: building and genotyping loci de novo from short-read sequences.
G3: Genes, Genomes, Genetics, 1:171-182, 2011