Selecting RAD-Seq Data Analysis Parameters for Population Genetics: The More the Better?

ABSTRACT: Restriction site-associated DNA sequencing (RAD-seq) has become a powerful and widely used tool in molecular ecology studies as it allows to cost-effectively recover thousands of polymorphic sites across individuals of non-model organisms. However, its successful implementation in population genetics relies on correct data processing that would minimize potential loci-assembly biases and consequent genotyping error rates. RAD-seq data processing when no reference genome is available involves the assembly of hundreds of thousands high-throughput sequencing reads into orthologous loci, for which various key parameter values need to be selected by the researcher. Previous studies exploring the effect of these parameter values found or assumed that a larger number of recovered polymorphic loci

SUBMITTER: Diaz-Arce N 

PROVIDER: S-EPMC6549478 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature