Abstract High-throughput sequencing technologies provide unprecedented power to identify novel viruses from a wide variety of (environmental) samples. The field of ‘viral metagenomics’ has dramatically expanded our understanding of viral diversity. Viral metagenomic approaches imply that many novel viruses will not be described by researchers who are experts on (the genomic organization of) that virus family. We have developed the papillomavirus annotation tool (PuMA) to provide researchers with a convenient and reproducible method to annotate and report novel papillomaviruses. PuMA currently correctly annotates 99% of the papillomavirus genes when benchmarked against the 655 reference genomes in the papillomavirus episteme. Compared to another viral annotation pipeline, PuMA annotates more viral features while being more accurate. To demonstrate its general applicability, we also developed a preliminary version of PuMA that can annotate polyomaviruses. PuMA is available on GitHub (https://github.com/KVD-lab/puma) and through the iMicrobe online environment (https://www.imicrobe.us/#/apps/puma).

中文翻译：

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PuMA：一种乳头瘤病毒基因组注释工具

摘要 高通量测序技术提供了前所未有的能力，可以从各种（环境）样本中识别新型病毒。“病毒宏基因组学”领域极大地扩展了我们对病毒多样性的理解。病毒宏基因组方法意味着许多新病毒不会被该病毒家族（其基因组组织）方面的专家的研究人员描述。我们开发了乳头瘤病毒注释工具 (PuMA)，为研究人员提供了一种方便且可重复的方法来注释和报告新型乳头瘤病毒。当与 papillomavirus episteme 中的 655 个参考基因组进行基准比较时，PuMA 目前正确注释了 99% 的 papillomavirus 基因。与另一个病毒注释管道相比，PuMA 注释了更多的病毒特征，同时更准确。为了证明其普遍适用性，我们还开发了可以注释多瘤病毒的 PuMA 的初步版本。PuMA 可在 GitHub (https://github.com/KVD-lab/puma) 和 iMicrobe 在线环境 (https://www.imicrobe.us/#/apps/puma) 上获得。