Ten practical guidelines for classifying unknown bacteriophages from genomic data
By
Fabian T. S. Bastiaanssen ,
Summary
This article provides ten practical tips for classifying unknown bacteriophages (viruses that infect bacteria). It covers the entire classification workflow, from initial sequence quality control and assembly, through taxonomic assignment using tools like vConTACT and geNomad, to phylogenetic analysis and functional annotation. The authors emphasize best practices for handling metagenomic data, avoiding common pitfalls like contamination, and leveraging databases such as ICTV and IMG/VR. The piece is written as a tutorial-style guide aimed at researchers and students in microbiology and virology, combining technical depth with accessible advice for newcomers to phage genomics.
Source
bskyTen practical guidelines for classifying unknown bacteriophages from genomic datajournals.plos.orgKey quotes
· 5 pulledClassifying unknown bacteriophages is a critical step in understanding the viral dark matter that dominates our biosphere.
The choice of reference database can dramatically alter the outcome of taxonomic assignment, and researchers should be aware of the biases inherent in each.
Metagenomic assemblies often contain fragmented or incomplete phage genomes, requiring careful quality filtering before classification.
Phage taxonomy is rapidly evolving, and tools developed just a few years ago may already be outdated.
A combination of marker-gene based and genome-wide approaches provides the most robust classification framework.
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