title: AftrRAD: a pipeline for accurate and efficient de novo assembly of RADseq data.
abstract: 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.
authors: Department of Evolution, Ecology, and Organismal Biology, Aronoff Laboratory, The Ohio State University, 318 W. 12th Ave, Columbus, OH, 43210, USA.|Ohio Biodiversity Conservation Partnership, Aronoff Laboratory, The Ohio State University, 318 W. 12th Ave, Columbus, OH, 43210, USA.
authors: Michael G
authors: MG
authors: Sovic
authors: Department of Evolution, Ecology, and Organismal Biology, Aronoff Laboratory, The Ohio State University, 318 W. 12th Ave, Columbus, OH, 43210, USA.
authors: Anthony C
authors: AC
authors: Fries
authors: Department of Evolution, Ecology, and Organismal Biology, Aronoff Laboratory, The Ohio State University, 318 W. 12th Ave, Columbus, OH, 43210, USA.|Ohio Biodiversity Conservation Partnership, Aronoff Laboratory, The Ohio State University, 318 W. 12th Ave, Columbus, OH, 43210, USA.
authors: H Lisle
authors: HL
authors: Gibbs
mesh_terms: D019295:Computational Biology / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
keywords: RADseq; bioinformatics; de novo assembly; genotyping; locus identification