aTRAM - automated Target Restricted Assembly Method: a fast method for assembling loci across divergent taxa from next-generation sequencing data

Background: Assembling genes from next-generation sequencing data is not only time consuming but computationally difficult, particularly for taxa without a closely related reference genome. Assembling even a draft genome using de novo approaches can take days, even on a powerful computer, and these assemblies typically require data from a variety of genomic libraries. Here we describe software that will alleviate these issues by rapidly assembling genes from distantly related taxa using a single library of paired-end reads: aTRAM, automated Target Restricted Assembly Method. The aTRAM pipeline uses a reference sequence, BLAST, and an iterative approach to target and locally assemble the genes of interest. Results: Our results demonstrate that aTRAM rapidly assembles genes across distantly related taxa. In comparative tests with a closely related taxon, aTRAM assembled the same sequence as reference-based and de novo approaches taking on average < 1 min per gene. As a test case with d...研究背景：从下一代测序（next-generation sequencing）数据中组装基因不仅耗时且计算复杂度极高，对于缺乏近缘参考基因组的分类群（taxa）而言尤为困难。即便采用从头组装（de novo）方法构建草图基因组，即便在高性能计算机上运行，往往也需要数日时间，且这类组装通常需要多种基因组文库的数据。本研究介绍一款可缓解上述问题的软件——aTRAM（自动化目标限制性组装方法，automated Target Restricted Assembly Method），其可依托单份配对末端读段（paired-end reads）文库，快速完成远缘分类群的基因组装。aTRAM流程借助参考序列、BLAST（碱基局部比对搜索工具，Basic Local Alignment Search Tool）以及迭代策略，实现目标基因的靶向定位与局部组装。 研究结果：本研究结果证实，aTRAM可快速完成远缘分类群的基因组装。在针对近缘分类群的对照测试中，aTRAM所获得的组装序列与基于参考基因组的组装方法及从头组装方法所得序列完全一致，单基因平均组装耗时不足1分钟。作为某测试案例的初步结果显示...