title: Stacks: an analysis tool set for population genomics.
abstract: Massively parallel short-read sequencing technologies, coupled with powerful software platforms, are enabling investigators to analyse tens of thousands of genetic markers. This wealth of data is rapidly expanding and allowing biological questions to be addressed with unprecedented scope and precision. The sizes of the data sets are now posing significant data processing and analysis challenges. Here we describe an extension of the Stacks software package to efficiently use genotype-by-sequencing data for studies of populations of organisms. Stacks now produces core population genomic summary statistics and SNP-by-SNP statistical tests. These statistics can be analysed across a reference genome using a smoothed sliding window. Stacks also now provides several output formats for several commonly used downstream analysis packages. The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.
authors.affiliation: Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA.
authors.forename: Julian
authors.initials: J
authors.lastname: Catchen
authors.forename: Paul A
authors.initials: PA
authors.lastname: Hohenlohe
authors.forename: Susan
authors.initials: S
authors.lastname: Bassham
authors.forename: Angel
authors.initials: A
authors.lastname: Amores
authors.forename: William A
authors.initials: WA
authors.lastname: Cresko
mesh_terms: D030561:Databases, Nucleic Acid; D001330:Electronic Data Processing / Q000379:methods*; D005819:Genetic Markers; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D056186:Metagenomics / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D005819:Genetic Markers