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Thank you for your interest in PhageScanner! This wiki contains information on installing and running the tool, in addition to examples of usage. Overall, this wiki can be used as the official documentation for the tool and will improve over time. If you'd like to quickly get started without visiting the other Wiki pages, please visit the Quick Start Guide Wiki page first.

Installation

NOTE: PhageScanner is only available on 64-bit macos and Ubuntu linux. To run the tool on windows, we recommend using the provided Docker image OR installing the Ubuntu Windows Subsystem for Linux (WSL). This limitation is due to some of the underlying tools PhageScanner uses, including: cd-hit, phanotate, and megahit. These all have C++ dependencies that are not inherently available on windows.

• PhageScanner Installation Guide

Using Each Pipeline

There are three fundamental pipelines in the PhageScanner tool. Each of these pipelines feeds into the next: (1) Download the training dataset, (2) Training the machine learning models, (3) Using the models to annotate genomes and metagenomics datasets. Each pipelines is configurable to allow end-users extreme flexibility in creating new models to predict new variations of protein classes (ex. "Toxic Protein", "Phage Virion Protein", "Lysogenic").

• Step 1 - Database Pipeline
• Step 2 - Training Pipeline
• Step 3 - Predict Pipeline