  Bacteriophages, which are viruses infecting bacteria, are the most ubiquitous
and diverse entities in the biosphere. There is accumulating evidence revealing
their important roles in shaping the structure of various microbiomes. Thanks
to (viral) metagenomic sequencing, a large number of new bacteriophages have
been discovered. However, lacking a standard and automatic virus classification
pipeline, the taxonomic characterization of new viruses seriously lag behind
the sequencing efforts. In particular, according to the latest version of ICTV,
several large phage families in the previous classification system are removed.
Therefore, a comprehensive review and comparison of taxonomic classification
tools under the new standard are needed to establish the state-of-the-art. In
this work, we retrained and tested four recently published tools on newly
labeled databases. We demonstrated their utilities and tested them on multiple
datasets, including the RefSeq, short contigs, simulated metagenomic datasets,
and low-similarity datasets. This study provides a comprehensive review of
phage family classification in different scenarios and a practical guidance for
choosing appropriate taxonomic classification pipelines. To our best knowledge,
this is the first review conducted under the new ICTV classification framework.
The results show that the new family classification framework overall leads to
better-conserved groups and thus makes family-level classification more
feasible.
