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Aftr RAD : a pipeline for accurate and efficient de novo assembly of RAD seq data
Author(s) -
Sovic Michael G.,
Fries Anthony C.,
Gibbs H. Lisle
Publication year - 2015
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12378
Subject(s) - indel , biology , pipeline (software) , computational biology , set (abstract data type) , sequence assembly , indel mutation , computer science , data mining , genetics , genotype , gene , programming language , single nucleotide polymorphism , transcriptome , gene expression
An increase in studies using restriction site‐associated DNA sequencing ( RAD seq) 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 Aftr RAD , a bioinformatic pipeline that efficiently assembles and genotypes RAD seq data, and outputs these data in various formats for downstream analyses. We use simulated and experimental data sets to evaluate Aftr RAD '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 Aftr RAD is able to accurately assemble loci, while accounting for indel variation among alleles, in a more computationally efficient manner than currently available programs. Aftr RAD 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.