pharokka

pharokka is a fast phage annotation pipeline.

phold

If you like pharokka, you will probably love phold. phold uses structural homology to improve phage annotation. Benchmarking is ongoing but phold strongly outperforms pharokka in terms of annotation, particularly for less characterised phages such as those from metagenomic datasets.

pharokka still has features phold lacks for now (identifying tRNA, tmRNA, CRISPR repeats, and INPHARED taxonomy search), so it it recommended to run phold after running pharokka.

phold takes the Genbank output of Pharokka as input. Therefore, if you have already annotated your phage(s) with Pharokka, you can easily update the annotation with more functional predictions with phold.

Overview

pharokka uses PHANOTATE, the only gene prediction program tailored to bacteriophages, as the default program for gene prediction. Prodigal implemented with pyrodigal and Prodigal-gv implemented with pyrodigal-gv are also available as alternatives. Following this, functional annotations are assigned by matching each predicted coding sequence (CDS) to the PHROGs, CARD and VFDB databases using MMseqs2. As of v1.4.0, pharokka will also match each CDS to the PHROGs database using more sensitive Hidden Markov Models using PyHMMER. Pharokka's main output is a GFF file suitable for using in downstream pangenomic pipelines like Roary. pharokka also generates a cds_functions.tsv file, which includes counts of CDSs, tRNAs, tmRNAs, CRISPRs and functions assigned to CDSs according to the PHROGs database. See the full usage and check out the full documentation for more details.

Manuscript

For more information, please read the pharokka manuscript:

George Bouras, Roshan Nepal, Ghais Houtak, Alkis James Psaltis, Peter-John Wormald, Sarah Vreugde, Pharokka: a fast scalable bacteriophage annotation tool, Bioinformatics, Volume 39, Issue 1, January 2023, btac776, https://doi.org/10.1093/bioinformatics/btac776

Google Colab Notebook

If you don't want to install pharokka locally, you can run it without any code using one this Google Colab notebook.

Pharokka, Phold and Phynteny are complimentary tools and when used together, they substantially increase the annotation rate of your phage genome. The below plot shows the annotation rate of different tools across 4 benchmarked datasets ((a) INPHARED 1419, (b) Cook, (c) Crass and (d) Tara - see the Phold preprint for more information)

Specifically, the final Phynteny plots combine the benefits of annotation with Pharokka (with HMM, the second violin) followed by Phold (with structures, the fourth violin) followed by Phynteny