Fig. 1

Overview of RefSeq benchmarking workflow. All bacterial and archaeal chromosomes and plasmids and phage genomes that were deposited in the RefSeq database between 1 January 2020 and 12 August 2021 inclusive were downloaded. The phage genomes were used to create a positive test set and the chromosomes and plasmids for a negative set. The sequences were dereplicated with the training sets for each machine/deep learning tool that was benchmarked (highlighted in red), as well as any RefSeq sequences deposited prior to 2020. The negative set was down sampled to produce a positive:negative ratio of approximately 1:19 to replicate a typical gut microbiome. Prophages were identified and removed with Phigaro and PhageBoost. Any host sequences with greater than 30% of open read frames having hits to the Prokaryotic Virus Orthologous Groups database were then removed. All sequences were then uniformly fragmented into artificial contigs with lengths between 1 and 15 kbp. All identification tools were then run on the artificial contig sets