taxmyPHAGE: Automated taxonomy of dsDNA phage genomes at the genus and species level

Abstract

Abstract Background Bacteriophages are now classified into genera and species based on genomic similarity. To identify new species and genera requires comparison against all phage genomes currently defined by the International Committee on the Taxonomy of Viruses. With increasing amounts of phage genomic data there is a clear need to fully automate the classification of phages into existing and new genera and species. Materials and Methods We created a MASH database for rapid searching of closely related phages, to then be compared with BLASTn to compute intergenomic similarity between bacteriophages ( https://github.com/amillard/tax_myPHAGE/tree/main ). Results Taxmyphage is provided as a conda repository and via a user-friendly website, that allows rapid classification of phages into existing taxa at the genus and species level. Conclusions Taxmyphage allows the rapid and accurate classification of phage genomes into existing genera and species, at a scale that is compatible with existing sequencing output.