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Bacteriophage Genome Annotation

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posted on 2021-11-05, 14:39 authored by Andrew MillardAndrew Millard, Anastasiya Shen

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)


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