Assembler for de novo assembly of large genomes
Assembler for de novo assembly of large genomes
复制标题
DOI：
10.1073/pnas.1314090110
复制
发表时间：
2013-09-03
影响因子：
11.1
通讯作者：
Shih, Arthur Chun-Chieh
中科院分区：
文献类型：
--
作者：
Chu, Te-Chin;Lu, Chen-Hua;Shih, Arthur Chun-Chieh
使用下一代测序读段组装大基因组需要大的计算机存储器和长的执行时间。为了减少这些要求，我们提出了一个基于扩展的汇编器，称为JR汇编器，其中J和R代表“跳跃”扩展和阅读“重映射”。首先，它使用读取计数来选择高质量的读取作为种子。其次，它通过全读段延伸过程来延伸每个种子，这加快了延伸过程，并且可以跳过短重复。第三，它使用动态后修剪过程来避免由于测序错误而导致的延伸终止。第四，它将读段重新映射到每个组装的序列，并且如果由于重复的存在而发生组装错误，则它在重复边界处破坏重叠群。第五，它采用不太严格的扩展标准来连接低覆盖区域。最后，它通过未使用的读段合并重叠群。广泛的比较JR-汇编器与目前的汇编器使用的数据集，从小型，中型和大型基因组表明，JR-汇编器实现了更好的或可比的整体组装质量，需要更低的内存使用和更少的中央处理单元的时间，特别是对于大型基因组。最后，模拟研究表明，JR-汇编器实现了上级性能的内存使用和中央处理单元的时间比大多数当前的汇编器时，读取长度为150 bp或更长，表明JR-汇编器的优势，目前的汇编器将增加读取长度的增加，随着下一代测序技术的进步。
Assembling a large genome using next generation sequencing reads requires large computer memory and a long execution time. To reduce these requirements, we propose an extension-based assembler, called JR-Assembler, where J and R stand for "jumping" extension and read "remapping." First, it uses the read count to select good quality reads as seeds. Second, it extends each seed by a whole-read extension process, which expedites the extension process and can jump over short repeats. Third, it uses a dynamic back trimming process to avoid extension termination due to sequencing errors. Fourth, it remaps reads to each assembled sequence, and if an assembly error occurs by the presence of a repeat, it breaks the contig at the repeat boundaries. Fifth, it applies a less stringent extension criterion to connect low-coverage regions. Finally, it merges contigs by unused reads. An extensive comparison of JR-Assembler with current assemblers using data-sets from small, medium, and large genomes shows that JR-Assembler achieves a better or comparable overall assembly quality and requires lower memory use and less central processing unit time, especially for large genomes. Finally, a simulation study shows that JR-Assembler achieves a superior performance on memory use and central processing unit time than most current assemblers when the read length is 150 bp or longer, indicating that the advantages of JR-Assembler over current assemblers will increase as the read length increases with advances in next generation sequencing technology.