Metagenomics and single‐cell genomics have enabled the discovery of relevant uncultured microbes. Recently, single‐virus genomics (SVG), although still in an incipient stage, has opened new avenues in viral ecology by allowing the sequencing of one single virus at a time. The investigation of methodological alternatives and optimization of existing procedures for SVG is paramount to deliver high‐quality genomic data. We report a sequencing dataset of viral single‐amplified genomes (vSAGs) from cultured and uncultured viruses obtained by applying different conditions in each SVG step, from viral preservation and novel whole‐genome amplification (WGA) to sequencing platforms and genome assembly. Sequencing data showed that cryopreservation and mild fixation were compatible with WGA, although fresh samples delivered better genome quality data. The novel TruPrime WGA, based on primase‐polymerase features, and WGA‐X employing a thermostable phi29 polymerase, were proven to be with sufficient sensitivity in SVG. The Oxford Nanopore (ON) sequencing platform did not provide a significant improvement of vSAG assembly compared to Illumina alone. Finally, the SPAdes assembler performed the best. Overall, our results represent a valuable genomic dataset that will help to standardized and advance new tools in viral ecology.

中文翻译：

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单病毒基因组学的基准测试：揭示病毒圈的新工具

宏基因组学和单细胞基因组学使相关未培养微生物的发现成为可能。最近，单病毒基因组学（SVG）虽然仍处于起步阶段，但通过允许一次对一种病毒进行测序，开辟了病毒生态学的新途径。研究 SVG 的方法替代方案和优化现有程序对于提供高质量的基因组数据至关重要。我们报告了一个来自培养和未培养病毒的病毒单扩增基因组 (vSAG) 测序数据集，该数据集通过在每个 SVG 步骤中应用不同条件获得，从病毒保存和新型全基因组扩增 (WGA) 到测序平台和基因组组装。测序数据显示，冷冻保存和温和固定与 WGA 兼容，尽管新鲜样本提供了更好的基因组质量数据。基于引物聚合酶特征的新型 TruPrime WGA 和采用热稳定 phi29 聚合酶的 WGA-X 被证明在 SVG 中具有足够的灵敏度。与单独的 Illumina 相比，Oxford Nanopore (ON) 测序平台没有显着改善 vSAG 组装。最后，SPAdes 汇编器表现最好。总体而言，我们的结果代表了一个有价值的基因组数据集，将有助于标准化和推进病毒生态学中的新工具。