Evaluation of viral genome assembly and diversity estimation in deep metagenomes.
Evaluation of viral genome assembly and diversity estimation in deep metagenomes.
复制标题
DOI：
10.1186/1471-2164-15-989
复制
发表时间：
2014-11-18
期刊：
影响因子：
4.4
通讯作者：
Alcamí A
中科院分区：
文献类型：
--
作者：
Aguirre de Cárcer D;Angly FE;Alcamí A
病毒具有独特的性质，小的基因组和高度相似的区域，其对宏基因组组装的影响迄今尚未被表征。本研究使用不同的计算机模拟病毒组，以评估如何广泛的基因组可以使用不同的测序平台和组装。此外，它调查了不同的方法来估计宏基因组中的病毒多样性的适用性。我们在不同的测序深度模拟各种平台创建了计算机宏基因组。与宏基因组特异性的IDBA_UD和CAMERA相比，CLC组装器显示出低于标准。在达到饱和点之前，Illumina平台被证明比454平台更有能力重建大部分病毒基因组。读取长度是限制嵌合性的重要因素，而支架化略微提高了重叠群长度和准确性。宏基因组中各种病毒的基因组长度对基因组重建没有显著影响，但高度相似的基因组的共存是有害的。在评估多样性估计工具时，我们发现PHACCS的结果比CatchAll和聚类的结果更准确，这两个数量级都高于预期。应使用专门为宏基因组分析设计的组装子来促进高质量长重叠群的创建。尽管覆盖率可能很高，但科学家不应该期望总是获得完整的基因组，因为它们的重建可能会受到共存物种的阻碍，这些物种具有高度相似的基因组区域。进一步发展面向宏基因组学的组装器可能有助于在未来的研究中绕过这些限制。与此同时，由于缺乏完全重建的社区，估计病毒多样性的方法仍然存在。虽然测试的三种方法都没有绝对的精确度，但只有PHACCS被认为适合进行比较研究。本文的在线版本（doi：10.1186/1471-2164-15-989）包含补充材料，可供授权用户使用。
Viruses have unique properties, small genome and regions of high similarity, whose effects on metagenomic assemblies have not been characterized so far. This study uses diverse in silico simulated viromes to evaluate how extensively genomes can be assembled using different sequencing platforms and assemblers. Further, it investigates the suitability of different methods to estimate viral diversity in metagenomes. We created in silico metagenomes mimicking various platforms at different sequencing depths. The CLC assembler revealed subpar compared to IDBA_UD and CAMERA , which are metagenomic-specific. Up to a saturation point, Illumina platforms proved more capable of reconstructing large portions of viral genomes compared to 454. Read length was an important factor for limiting chimericity, while scaffolding marginally improved contig length and accuracy. The genome length of the various viruses in the metagenomes did not significantly affect genome reconstruction, but the co-existence of highly similar genomes was detrimental. When evaluating diversity estimation tools, we found that PHACCS results were more accurate than those from CatchAll and clustering, which were both orders of magnitude above expected. Assemblers designed specifically for the analysis of metagenomes should be used to facilitate the creation of high-quality long contigs. Despite the high coverage possible, scientists should not expect to always obtain complete genomes, because their reconstruction may be hindered by co-existing species bearing highly similar genomic regions. Further development of metagenomics-oriented assemblers may help bypass these limitations in future studies. Meanwhile, the lack of fully reconstructed communities keeps methods to estimate viral diversity relevant. While none of the three methods tested had absolute precision, only PHACCS was deemed suitable for comparative studies. The online version of this article (doi:10.1186/1471-2164-15-989) contains supplementary material, which is available to authorized users.
登录
查看更多内容
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
Metasim：用于基因组学和元基因组学的测序模拟器。
影响因子：
3.7
作者：
Richter, Daniel C.;Ott, Felix;Auch, Alexander F.;Schmid, Ramona;Huson, Daniel H.
通讯作者：
Huson, Daniel H.
影响因子：
4.4
作者：
McElroy KE;Luciani F;Thomas T
通讯作者：
Thomas T
DOI：
10.1098/rstb.2006.1920
发表时间：
2006-11-29
影响因子：
6.3
作者：
Konstantinidis, Konstantinos T.;Ramette, Alban;Tiedje, James M.
通讯作者：
Tiedje, James M.
影响因子：
15.5
作者：
Allen, Heather K.;Bunge, John;Stanton, Thaddeus B.
通讯作者：
Stanton, Thaddeus B.