Published September 13, 2025 | Version v4
Dataset Open

Pharokka Database v1.8.0

Authors/Creators

  • 1. University of Adelaide

Description

This holds the databases for Pharokka v1.8.0 (https://github.com/gbouras13/pharokka). 

It includes the PHROGs profile database made with MMSeqs2 (v18.8cc5c) and PHROGs HMM database made with Pyhmmer (v0.9.0 - .h3m file of all 38880 PHROGs), along with MMseqs2 compatible versions of the CARD v3.2.7 and VFDB (as of August 18 2023) databases.

The VFDB database has been clustered using MMSeqs2 at 50% sequence identity to reduce its size and speed up Pharokka's runtime.

`mmseqs easy-cluster VFDB_setB_pro_form.fas VFDBclusterRes tmp --min-seq-id 0.5 -c 0.8 --cov-mode 1`

It also includes the INPHARED mash sketch and annotation file current as of 9 August 2025 (https://github.com/RyanCook94/inphared  https://millardlab.org/bacteriophage-genomics/phage-genomes-aug-2025/). 

Files

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