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Stacks: an analysis tool set for population genomics
Author(s) -
Catchen Julian,
Hohenlohe Paul A.,
Bassham Susan,
Amores Angel,
Cresko William A.
Publication year - 2013
Publication title -
molecular ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.619
H-Index - 225
eISSN - 1365-294X
pISSN - 0962-1083
DOI - 10.1111/mec.12354
Subject(s) - population genomics , genomics , biology , software , massively parallel , massive parallel sequencing , population , snp genotyping , computer science , set (abstract data type) , genotyping , computational biology , dna sequencing , data science , genome , genetics , genotype , programming language , dna , demography , sociology , parallel computing , gene
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 S tacks 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 S tacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.