Data from: AftrRAD: a pipeline for accurate and efficient de novo assembly of RADseq data

An increase in studies using restriction site-associated DNA sequencing
(RADseq) methods has led to a need for both the development and assessment
of novel bioinformatic tools that aid in the generation and analysis of
these data. Here, we report the availability of AftrRAD, a bioinformatic
pipeline that efficiently assembles and genotypes RADseq data, and outputs
these data in various formats for downstream analyses. We use simulated
and experimental data sets to evaluate AftrRAD's ability to perform
accurate de novo assembly of loci, and we compare its performance with two
other commonly used programs, stacks and pyrad. We demonstrate that
AftrRAD is able to accurately assemble loci, while accounting for indel
variation among alleles, in a more computationally efficient manner than
currently available programs. AftrRAD run times are not strongly affected
by the number of samples in the data set, making this program a useful
tool when multicore systems are not available for parallel processing, or
when data sets include large numbers of samples.