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

SUBMITTER: Puritz JB 

PROVIDER: S-EPMC4060032 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature