Pharokka v 1.1.0 Benchmarking Input Output and Script

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.