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).
Highlights
Viruses and viral diseases have fascinated humans for millennia (reviewed in (Woolhouse et al, 2012)
We are currently in the era of ‘Neovirology’ (Enquist and Editors of the Journal of Virology, 2009), and recent technological advances provide an agnostic approach to sequencing nucleotides from environmental samples
We developed PuMA to generate consistent and uniformly annotated papillomavirus genomes
Summary
Viruses and viral diseases have fascinated humans for millennia (reviewed in (Woolhouse et al, 2012). We are currently in the era of ‘Neovirology’ (Enquist and Editors of the Journal of Virology, 2009), and recent technological advances provide an agnostic approach to sequencing nucleotides from environmental samples. These approaches dramatically accelerated viral discovery (Hurwitz et al, 2016; Nooij et al, 2018). Approaches facilitate the identification of highly diverse viruses from a wide array of sample types. For these viromic studies to maximize their potential scientific impact, the identified viral genomes should be annotated and curated prior to publication. These software tools should be universally available, actively maintained, powerful yet intuitive, and automatable (Rose et al, 2016)
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