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.

随着采用限制性酶切位点相关DNA测序（restriction site-associated DNA sequencing, RADseq）方法的研究日益增多，学界亟需开发并评估可辅助此类数据生成与分析的新型生物信息学工具。本研究介绍了AftrRAD——一款可高效组装并对RADseq数据进行基因分型的生物信息学流程，其支持以多种格式输出数据以供后续分析。本研究通过模拟数据集与实验数据集，评估AftrRAD对基因座进行精准从头组装的能力，并将其性能与两款常用软件stacks和pyrad进行对比。研究表明，相较于现有工具，AftrRAD可在考虑等位基因间插入缺失变异的前提下，精准完成基因座组装，且计算效率更优。AftrRAD的运行时长不受样本量的显著影响，因此在无法使用多核系统开展并行处理，或数据集样本量庞大时，该软件均是一款实用的分析工具。