Quick Start

This guide will help you get started with PhiSpy quickly.

Testing PhiSpy

To test that PhiSpy is working correctly, download the Streptococcus pyogenes M1 genome:

curl -Lo Streptococcus_pyogenes_M1_GAS.gb https://bit.ly/37qFArb
PhiSpy.py -o Streptococcus.phages Streptococcus_pyogenes_M1_GAS.gb

This should identify four prophages in the genome.

To use a specific training set:

PhiSpy.py -o Streptococcus.phages -t data/trainSet_160490.61.txt Streptococcus_pyogenes_M1_GAS.gb

Basic Usage

The simplest command to run PhiSpy is:

PhiSpy.py genbank_file -o output_directory

Where:

  • genbank_file: The input DNA sequence file in GenBank format

  • output_directory: The directory where output files will be created

Preparing Your Genome

PhiSpy requires an annotated genome in GenBank format. If you have a new genome that needs annotation, we recommend:

  1. RAST (http://rast.nmpdr.org/rast.cgi) - A web server that allows you to upload and download annotated genomes

  2. PROKKA (https://github.com/tseemann/prokka) - Stand-alone annotation software

Example Workflow

  1. Annotate your genome using RAST or PROKKA

  2. Run PhiSpy with default parameters:

    PhiSpy.py my_genome.gb -o phispy_results

  3. Review the output files in the phispy_results directory

  4. Adjust parameters if needed and re-run

Common Use Cases

Find prophages with default settings:

PhiSpy.py genome.gb -o results

Find prophages and color CDSs for Artemis visualization:

PhiSpy.py genome.gb -o results --color

Find prophages using HMM profiles:

PhiSpy.py genome.gb -o results --phmms pVOGs.hmm --threads 4

Get all output files:

PhiSpy.py genome.gb -o results --output_choice 512

Next Steps