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专业背景:计算机科学 研究方向与兴趣: JavaEE-Web软件开发, 生物信息学, 数据挖掘与机器学习, 智能信息系统 目前工作: 基因组, 转录组, NGS高通量数据分析, 生物数据挖掘, 植物系统发育和比较进化基因组学

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最新大基因组组装软件 JR-Assembler  

2013-08-28 15:14:08|  分类: 生信分析软件 |  标签: |举报 |字号 订阅

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Assembler for de novo assembly of large genomes
文章链接:
http://www.pnas.org/content/early/2013/08/21/1314090110.long


摘要
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 datasets 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.

根据文章的分析结果显示,要比Velvet 和SOAPdenovo组装要好一些。它已集成了SSPACE程序。当然,自己在基因组组装时,也可以用Velvet和SOAPdenovo组装后,再用SSPACE链接,目前通常都要做这一步。我想这样的组装结果应该和JR-Asssember的组装结果差不多,但是文章中没有比较。
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