A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.
A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.
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DOI：
10.1371/journal.pone.0017915
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发表时间：
2011-03-14
期刊：
影响因子：
3.7
通讯作者：
Shen B
中科院分区：
文献类型：
--
作者：
Zhang W;Chen J;Yang Y;Tang Y;Shang J;Shen B
新一代测序技术的出现伴随着许多全基因组序列组装方法和软件的发展，特别是从头开始的片段组装。由于对这些软件工具的适用性和性能知之甚少，选择合适的汇编器成为一项艰巨的任务。在这里，我们提供了每个程序的适应性信息，然后首先比较了八种不同工具与Solexa测序平台的八组模拟数据集的性能。我们的研究表明，在计算时间、最大随机存取存储器(RAM)占用率、组装精度和完整性方面，基于字符串的汇编程序和重叠布局一致(OLC)汇编程序分别适合于小基因组的很短和较长的读取。对于超过亿次短读的大型数据集，基于de Bruijn图的汇编程序将更合适。在软件实现方面，基于串的汇编器优于基于图的汇编器，其中SOAPdenovo对于配置文件的创建是复杂的。我们的对比研究将有助于研究人员选择合适的装配机，并为现有装配机的改进或新型装配机的开发提供必要的信息。
The advent of next-generation sequencing technologies is accompanied with the development of many whole-genome sequence assembly methods and software, especially for de novo fragment assembly. Due to the poor knowledge about the applicability and performance of these software tools, choosing a befitting assembler becomes a tough task. Here, we provide the information of adaptivity for each program, then above all, compare the performance of eight distinct tools against eight groups of simulated datasets from Solexa sequencing platform. Considering the computational time, maximum random access memory (RAM) occupancy, assembly accuracy and integrity, our study indicate that string-based assemblers, overlap-layout-consensus (OLC) assemblers are well-suited for very short reads and longer reads of small genomes respectively. For large datasets of more than hundred millions of short reads, De Bruijn graph-based assemblers would be more appropriate. In terms of software implementation, string-based assemblers are superior to graph-based ones, of which SOAPdenovo is complex for the creation of configuration file. Our comparison study will assist researchers in selecting a well-suited assembler and offer essential information for the improvement of existing assemblers or the developing of novel assemblers.
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