dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

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 .

Fine-scale partitioning of genomic variation among recruits in an exploited fishery: causes and consequences

“…; details may be found in Supplementary Methods. Assembly, mapping, and SNP genotyping employed the dDocent pipeline17. The initial dataset consisted of 339,032 variant SNP loci across 38,122 fragments.…”

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions

“…A second set of methods for reduced representation uses restriction enzymes to isolate small pieces of DNA (such as restriction-associated digest sequencing [RAD-seq] or genotyping by sequencing [GBS; reviewed in Puritz et al 2014b; Andrews et al 2016]; table A2). These methods are useful for building genetic linkage maps and establishing neutral patterns of population structure (Andolfatto et al 2011; El-shire et al 2011).…”

Guidelines for planning genomic assessment and monitoring of locally adaptive variation to inform species conservation

“…This choice will determine the appropriate type of assembly program to use (e.g., GATK: McKenna et al., 2010; dePristo et al., 2011; Van der Auwera et al., 2013 with a reference genome; Stacks: Catchen, Amores, Hohenlohe, Cresko, & Postlethwait, 2011; Catchen, Hohenlohe, Bassham, Amores, & Cresko, 2013; Paris, Stevens, & Catchen, 2017; or dDocent: Puritz, Hollenbeck, & Gold, 2014 for a de novo assembly). Using a high‐quality and well‐annotated reference genome facilitates the identification of candidate genes and gene regions and allows for a truly genomic approach (e.g., considering physical linkage between regions with adaptive variation; Manel et al., 2016).…”