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

Abstract

14Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful 15 approach for population genomics. Currently, no software exists that utilizes both paired-end 16 reads from RADseq data to efficiently produce population-informative variant calls, 17 especially for organisms with large effective population sizes and high levels of genetic 18 polymorphism but for which no genomic resources exist. dDocent is an analysis pipeline with 19 a user-friendly, command-line interface designed to process individually barcoded RADseq 20 data (with double cut sites) into informative SNPs/INDELs for population-level analyses. The 21 pipeline, written in BASH, uses data reduction techniques and other stand-alone software 22packages to perform quality trimming and adapter removal, de novo assembly of RAD loci, 23 read mapping, SNP and INDEL calling, and baseline data filtering. Double-digest RAD data 24 from population pairings of three different marine fishes were used to compare dDocent with 25Stacks, the first generally available, widely used pipeline for analysis of RADseq data. 26 dDocent consistently identified more SNPs shared across greater numbers of individuals and 27 with higher levels of coverage. This is most likely due to the fact that dDocent quality trims 28 instead of filtering and incorporates both forward and reverse reads in assembly, mapping, 29 and SNP calling, thus enabling use of reads with INDEL polymorphisms. The pipeline and a 30 comprehensive user guide can be found at (http://dDocent.wordpress.com). 31 32PeerJ PrePrints | http://dx.doi.org/10.7287/peerj.preprints.314v1 | CC-BY 4.0

Population structure, genetic connectivity, and adaptation in the Olympia oyster (Ostrea lurida) along the west coast of North America

“…Population genetic summary statistics, with the exception of F ST , did change quantitatively due to missing data but not qualitatively (not shown) (Cariou, Duret, & Charlat, ). Filtering steps were conducted using VCFtools (Danecek et al., ), custom Python code, and code adapted from Jon Puritz's laboratory (Puritz, Hollenbeck, & Gold, ). Input files and formats for subsequent analysis of population structure were created using a combination of custom Python code, custom R code, and the radiator R package (Gosselin, ).…”

Major histocompatibility complex variation and blood parasites in resident and migratory populations of the common yellowthroat

“…), de novo assembly of RAD loci using cd‐hit (Fu et al ., ), read mapping back onto the de novo assembly using BWA mem (Li & Durbin, ), SNP calling using FreeBayes (Garrison & Marth, ) and, finally, variant filtering using VCFtools (Danecek et al ., ). We used dDocent, rather than Stacks (Catchen et al ., ), the other commonly used program, because dDocent identifies more SNPs as a consequence of using both forward and reverse reads during alignment and quality trimming instead of removing entire reads (Puritz et al ., ). We used default settings for most of the dDocent pipeline, except sequences were clustered at 95%, instead of 90% similarity.…”

“…Sequence reads were then prepared for the SNP analyses using version 2.17 of the dDocent pipeline (Puritz et al ., ) for initial filtering (phred quality scores < 33) and trimming using Trimmomatic (Bolger et al . ), de novo assembly of RAD loci using cd‐hit (Fu et al ., ), read mapping back onto the de novo assembly using BWA mem (Li & Durbin, ), SNP calling using FreeBayes (Garrison & Marth, ) and, finally, variant filtering using VCFtools (Danecek et al ., ).…”

Population Structure of Atlantic Croakers from the Gulf of Mexico: Evaluating a Single‐Stock Hypothesis Using a Genomic Approach

“…Quality trimming, assembly of a reduced representation reference, read mapping, and SNP calling were performed using the dDocent pipeline (Puritz et al. ). Two randomly chosen individuals from each sampling location ( n = 10 total) were used for de novo assembly of a reduced representation reference consisting of putatively orthologous loci.…”