dDocent

dDocent is simple bash wrapper to QC, assemble, map, and call SNPs from almost any kind of RAD sequencing. If you have a reference already, dDocent can be used to call SNPs from almost any type of NGS data set. It is designed to run on Linux based machines with large memory capacity and multiple processing cores, and it can be modified for use on HPC.

Why use dDocent?

Accuracy

de novo assembly

dDocent employs a series of data reduction techniques, aligment based clustering (using CD-hit), and, for PE assembly, a specialized RAD assembly software (rainbow. This combination allows for accurate and effecient de novo assembly.

Bayesian, haplotype based, population-aware, genotyping from FreeBayes

FreeBayes is a Bayesian genetic variant detector designed to detect SNPs, INDels (insertions and deletions), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. FreeBayes is haplotype-based, in the sense that it calls variants based on the literal sequences of reads aligned to a particular target, not their precise alignment, and for any number of individuals from a population and a to determine the most-likely combination of genotypes for the population at each position in the reference.