drVM: a new tool for efficient genome assembly of known eukaryotic viruses from metagenomes.
drVM: a new tool for efficient genome assembly of known eukaryotic viruses from metagenomes.
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DOI：
10.1093/gigascience/gix003
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发表时间：
2017-02-01
期刊：
影响因子：
9.2
通讯作者：
Liao YC
中科院分区：
文献类型：
--
作者：
Lin HH;Liao YC
背景：使用高通量下一代测序发现病毒已变得越来越普遍。然而，尽管对下一代测序数据的深入分析使我们能够识别潜在的病原体，但整个分析过程需要生物信息学领域的能力，包括实施适当的软件包和准备先决条件数据库。迫切需要简单和用户友好的生物信息学管道从宏基因组数据获得完整的病毒基因组序列。 结果如下：该手稿提出了一个管道，drVM（从宏基因组检测和重建已知的病毒基因组），用于快速病毒读段识别，基因级读段划分，读段标准化，从头组装，序列注释和覆盖率分析。前两个程序和序列注释依赖于已知的病毒基因组作为参考数据库。drVM通过分析Illumina和Ion Torrent平台生成的300多个测序运行进行了验证，可为各种病毒类型（包括DNA病毒、RNA病毒和逆转录病毒）提供完整的病毒基因组组装。drVM可从https://sourceforge.net/projects/sb2nhri/files/drVM/免费下载，并组装为Docker容器、Amazon机器映像和虚拟机，以促进无缝部署。 结论：drVM与其他病毒检测工具进行了比较，以证明其在病毒基因组完整性和减少计算时间方面的优点。这证实了该平台从临床样本中快速准确地产生病毒基因组序列的潜力。
Background: Virus discovery using high-throughput next-generation sequencing has become more commonplace. However, although analysis of deep next-generation sequencing data allows us to identity potential pathogens, the entire analytical procedure requires competency in the bioinformatics domain, which includes implementing proper software packages and preparing prerequisite databases. Simple and user-friendly bioinformatics pipelines are urgently required to obtain complete viral genome sequences from metagenomic data. Results: This manuscript presents a pipeline, drVM (detect and reconstruct known viral genomes from metagenomes), for rapid viral read identification, genus-level read partition, read normalization, de novo assembly, sequence annotation, and coverage profiling. The first two procedures and sequence annotation rely on known viral genomes as a reference database. drVM was validated via the analysis of over 300 sequencing runs generated by Illumina and Ion Torrent platforms to provide complete viral genome assemblies for a variety of virus types including DNA viruses, RNA viruses, and retroviruses. drVM is available for free download at: https://sourceforge.net/projects/sb2nhri/files/drVM/ and is also assembled as a Docker container, an Amazon machine image, and a virtual machine to facilitate seamless deployment. Conclusions: drVM was compared with other viral detection tools to demonstrate its merits in terms of viral genome completeness and reduced computation time. This substantiates the platform's potential to produce prompt and accurate viral genome sequences from clinical samples.