Journal
MOLECULAR ECOLOGY
Volume 28, Issue 21, Pages 4737-4754Publisher
WILEY
DOI: 10.1111/mec.15253
Keywords
bioinformatics; conservation genetics; genotype calling; haplotype phasing; population genetics; restriction-site associated DNA sequencing
Funding
- NSF [1645087]
- Directorate For Geosciences
- Office of Polar Programs (OPP) [1645087] Funding Source: National Science Foundation
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For half a century population genetics studies have put type II restriction endonucleases to work. Now, coupled with massively-parallel, short-read sequencing, the family of RAD protocols that wields these enzymes has generated vast genetic knowledge from the natural world. Here, we describe the first software natively capable of using paired-end sequencing to derive short contigs from de novo RAD data. Stacks version 2 employs a de Bruijn graph assembler to build and connect contigs from forward and reverse reads for each de novo RAD locus, which it then uses as a reference for read alignments. The new architecture allows all the individuals in a metapopulation to be considered at the same time as each RAD locus is processed. This enables a Bayesian genotype caller to provide precise SNPs, and a robust algorithm to phase those SNPs into long haplotypes, generating RAD loci that are 400-800 bp in length. To prove its recall and precision, we tested the software with simulated data and compared reference-aligned and de novo analyses of three empirical data sets. Our study shows that the latest version of Stacks is highly accurate and outperforms other software in assembling and genotyping paired-end de novo data sets.
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