A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data
A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data
复制标题
DOI：
10.1093/bioinformatics/btu661
复制
发表时间：
2015-02-15
期刊：
影响因子：
5.8
通讯作者：
Darling, Aaron E.
中科院分区：
文献类型：
--
作者：
Coil, David;Jospin, Guillaume;Darling, Aaron E.
动机：由于其复杂性，许多生物学家仍然无法获得开源细菌基因组组装。很少有软件解决方案存在，能够自动化的从头基因组assembly从Illumina data.Results的过程中的所有步骤：A5-miseq可以产生高品质的微生物基因组组装在笔记本电脑上没有任何参数调整。A5-miseq通过自动化适配器修剪、质量过滤、错误校正、重叠群和支架生成以及错误组装检测的过程来实现这一点。与原始A5流水线不同，A5-miseq可以使用来自Illumina MiSeq的长读段，在重叠群生成期间使用读段配对信息，并包括对读段修剪的几项改进。总之，这些变化导致大大改善的组装，恢复比以前的方法更完整的一组参考基因。
Motivation: Open-source bacterial genome assembly remains inaccessible to many biologists because of its complexity. Few software solutions exist that are capable of automating all steps in the process of de novo genome assembly from Illumina data.Results: A5-miseq can produce high-quality microbial genome assemblies on a laptop computer without any parameter tuning. A5-miseq does this by automating the process of adapter trimming, quality filtering, error correction, contig and scaffold generation and detection of misassemblies. Unlike the original A5 pipeline, A5-miseq can use long reads from the Illumina MiSeq, use read pairing information during contig generation and includes several improvements to read trimming. Together, these changes result in substantially improved assemblies that recover a more complete set of reference genes than previous methods.