This record contains all benchmarking input FASTA and output files for the Pharokka manuscript. Enterobacteria Phage Lambda (Genbank accession J02459), Staphylococcus phage SAOMS1 (Genbank accessionMW460250) and 673 crAss-like metagenome assembled phage genomes from the human gut taken from Yutin et al 2021 (https://doi.org/10.1038/s41467-021-21350-w). Each input was benchmarked with 3 runs: 1) Pharokka v1.1.0 using PHANOTATE as a gene predictor 2) Pharokka v1.1.0 specifying Prodigal as gene predictor, and 3) Prokka v1.14.6 using a version of the PHROGs HMM database that has been reformatted for use with Prokka found at the following URLs (http://s3.climb.ac.uk/ADM_share/all_phrogs.hmm.gz https://millardlab.org/2021/11/21/phage-annotation-with-phrogs/ ). Benchmarking was conducted on an Intel® Xeon® CPU E5-4610 v2 @ 2.30GHz specifying 16 threads for Pharokka and 16 cpus for Prokka. Coding densities for each contig in the Prokka output were calculated using the python script calc_gff_coding_density_prokka.py available in the tarball. Prokka coding densities are included in the Prokka_CDS_Coding_Densities directory.