Abstract
Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially for non-model organisms with large effective population sizes and high levels of genetic polymorphism. dDocent is an analysis pipeline with a user-friendly, command-line interface designed to process individually barcoded RADseq data (with double cut sites) into informative SNPs/Indels for population-level analyses. The pipeline, written in BASH, uses data reduction techniques and other stand-alone software packages to perform quality trimming and adapter removal, de novo assembly of RAD loci, read mapping, SNP and Indel calling, and baseline data filtering. Double-digest RAD data from population pairings of three different marine fishes were used to compare dDocent with Stacks, the first generally available, widely used pipeline for analysis of RADseq data. dDocent consistently identified more SNPs shared across greater numbers of individuals and with higher levels of coverage. This is due to the fact that dDocent quality trims instead of filtering, incorporates both forward and reverse reads (including reads with INDEL polymorphisms) in assembly, mapping, and SNP calling. The pipeline and a comprehensive user guide can be found at http://dDocent.wordpress.com.
Highlights
Next-generation sequencing (NGS) has transformed the field of genetics into genomics by providing DNA sequence data at an ever increasing rate and reduced cost (Mardis, 2008)
The most common approach, restriction-site associated DNA sequencing (RADseq), uses restriction endonucleases to randomly sample the genome at locations adjacent to restriction-enzyme recognition sites that, when coupled with Illumina sequencing, produces high coverage of homologous SNP (Single Nucleotide Polymorphism) loci
How to cite this article Puritz et al (2014), dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms
Summary
Next-generation sequencing (NGS) has transformed the field of genetics into genomics by providing DNA sequence data at an ever increasing rate and reduced cost (Mardis, 2008). The original RADseq approach (Baird et al, 2008; Miller et al, 2007), and initial population genomic studies employing it (Hohenlohe et al, 2010), focused on SNP discovery and genotyping on the first (forward) read only This is because the original RADseq method (Baird et al, 2008; Miller et al, 2007) utilized random shearing to produce RAD loci; paired-end reads were not of uniform length or coverage, making it problematic to find SNPs at high and uniform levels of coverage across a large proportion of individuals. DDocent is a wrapper script designed to take raw flRAD data and produce population informative SNP calls (SNPs that are shared across the majority of individuals and populations), taking full advantage of both paired-end reads. Results of pipeline analyses, using both dDocent and Stacks, of populations of three species of marine fishes are provided to demonstrate the utility of dDocent compared to Stacks, the first and most comprehensive, existing software package for RAD population genomics
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