Bacteriophage Genome Annotation

Reformatted PHROGs database Reformatting of the PHROGs database (https://phrogs.lmge.uca.fr/index.php) to allow it to be used within Prokka directly and output the PHROGS annotations to the “product” description in genbank files. All annotations are maintained from the PHROGs database set. File is called all_PHROGs.tar.gz Place in prokka-1.13-2/db/hmm/ to use with prokka Contained within this repository are worked examples for the assembly and annotation of a bacteriophage genome. Full detailed instructions are provided as part of the manuscript “Phage Genome annotation: where to begin and end” File: SRR13108336_Illumina.tar.gz contains all the files produced from the intermediary steps in the assembly and annotation of a phage genome from single end Illumina reads. Originally deposited by Milhaven et al (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8407768/) and used as an exemplar File: nanopore_example.tar.gz contains all the files produced from the intermediary steps in the assembly and annotation of a phage genome from nanopore data. Originally deposited by D`Souza et al (https://journals.asm.org/doi/10.1128/MRA.00730-20)