vRhyme enables binning of viral genomes from metagenomes.
vRhyme enables binning of viral genomes from metagenomes.
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DOI：
10.1093/nar/gkac341
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发表时间：
2022-08-12
影响因子：
14.9
通讯作者：
Anantharaman, Karthik
中科院分区：
文献类型：
--
作者：
Kieft, Kristopher;Adams, Alyssa;Salamzade, Rauf;Kalan, Lindsay;Anantharaman, Karthik
基因组分类对于细菌，古细菌，甚至真核生物的宏基因组的表征是必不可少的。然而，几乎没有针对病毒的方法。我们开发了vRhyme，一个快速和精确的软件，用于构建病毒宏基因组组装基因组（vMAGs）。vRhyme利用支架之间的单样本或多样本覆盖效应大小比较，并采用监督机器学习来识别核苷酸特征相似性，这些相似性被编译成加权网络和精炼箱的迭代。vRhyme利用病毒基因组的独特特征，即基于观察到病毒很少编码冗余基因的蛋白质冗余评分机制来改进箱。通过模拟病毒组，我们展示了vRhyme在构建更完整和无污染的vmag方面比现有的分箱工具更优越的性能。当应用于10,601个来自人体皮肤的病毒支架时，vRhyme提高了我们对居住病毒的理解，突出的是鉴定出由22个支架组成的Herelleviridae vMAG，以及另一个编码硝酸盐还原酶代谢基因的vMAG，代表了近乎完整的基因组。vRhyme将实现对未培养病毒基因组进行分类的惯例，并有可能改变基于宏基因组的病毒生态。
Genome binning has been essential for characterization of bacteria, archaea, and even eukaryotes from metagenomes. Yet, few approaches exist for viruses. We developed vRhyme, a fast and precise software for construction of viral metagenome-assembled genomes (vMAGs). vRhyme utilizes single- or multi-sample coverage effect size comparisons between scaffolds and employs supervised machine learning to identify nucleotide feature similarities, which are compiled into iterations of weighted networks and refined bins. To refine bins, vRhyme utilizes unique features of viral genomes, namely a protein redundancy scoring mechanism based on the observation that viruses seldom encode redundant genes. Using simulated viromes, we displayed superior performance of vRhyme compared to available binning tools in constructing more complete and uncontaminated vMAGs. When applied to 10,601 viral scaffolds from human skin, vRhyme advanced our understanding of resident viruses, highlighted by identification of a Herelleviridae vMAG comprised of 22 scaffolds, and another vMAG encoding a nitrate reductase metabolic gene, representing near-complete genomes post-binning. vRhyme will enable a convention of binning uncultivated viral genomes and has the potential to transform metagenome-based viral ecology.
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影响因子：
5.8
作者：
Arisdakessian, Cedric G.;Nigro, Olivia;Belcaid, Mahdi
通讯作者：
Belcaid, Mahdi
影响因子：
6.4
作者：
Barr, Jeremy J.
通讯作者：
Barr, Jeremy J.
影响因子：
14.9
作者：
Clark K;Karsch-Mizrachi I;Lipman DJ;Ostell J;Sayers EW
通讯作者：
Sayers EW
DOI：
10.1073/pnas.1305923110
发表时间：
2013-06-25
影响因子：
11.1
作者：
Barr, Jeremy J.;Auro, Rita;Rohwer, Forest
通讯作者：
Rohwer, Forest
影响因子：
15.5
作者：
Coutinho FH;Cabello-Yeves PJ;Gonzalez-Serrano R;Rosselli R;López-Pérez M;Zemskaya TI;Zakharenko AS;Ivanov VG;Rodriguez-Valera F
通讯作者：
Rodriguez-Valera F