GenomeProfiler

Welcome to GenomeProfiler! GenomeProfiler is an automated pipeline for the profiling of prokaryotes and plasmids, including gene annotation across a wide range of features. GenomeProfiler provides features and nucleotide coordinates of metadata features for easy use in visual profiling and other analyses. Current features include antibiotic resistance genes, virulence genes, mobile genetic elements, finding related plasmids (for plasmid input), and more.

Install

NOTE: Instructions are currently for linux-64 and osx-64 architectures.

Install Miniforge

Follow official instructions to install Miniforge.

Verify that Conda is available by printing its version: bash conda --version

Install GenomeProfiler

If you do not already have a Conda environment, create one: bash conda create --name myenv

Install the genome_profiler package from the bioconda channel: bash conda install --name myenv -c bioconda genome_profiler

Register Email with Entrez

Registering an email with Entrez is not necessary for use, and the GENPROF_ENTREZ_EMAIL environment variable (see Install GenomeProfiler) may be set to any valid email address. However, registration will allow for the processing of more accessions simultaneously in a given run. To register, visit the NCBI Entrez website and click "Log in". Create an account using your preferred email. If you do not wish to create an NCBI account, simply use a valid email. A later step will instruct you to include this email address in your .env file.

Get IslandViewer Token

(For the islandviewer tool.)

Visit the IslandViewer website to create an account and obtain an API token. Navigate to the "Login" tab and create an account or sign into an existing one. Once you are signed in, navigate to the "Jobs" tab and click "HTTP API Token". A later step will instruct you to include this token in your .env file. Note that this API token expires every 30 days and needs to be renewed.

Install Resources Used by GenomeProfiler

Navigate to the directory in which you want to install GenomeProfiler.

Environment variables used by GenomeProfiler may be written in .env. Create a file named .env and open it in a text editor (GNU nano depicted here): bash nano .env

Insert the following text into .env:

```bash

genome_profiler

GENPROFENTREZEMAIL= GENPROFISLANDVIEWERAUTH_TOKEN= ```

The entries of .env are as follows: - GENPROF_ENTREZ_EMAIL: your valid email address. - GENPROF_ISLANDVIEWER_AUTH_TOKEN: your API key from IslandViewer.

Insert your own value after each corresponding =. Save and exit.

Activate the Conda environment which genome_profiler is installed to: bash conda activate myenv

Install resources (databases etc.) used by GenomeProfiler to ./data_GenomeProfiler: bash genome_profiler --setup

Usage

Graphical Mode

Open GenomeProfiler in graphical mode: bash genome_profiler --gui

By default, GenomeProfiler will save its output to ./output_GenomeProfiler.

Command Line Interface

Print the GenomeProfiler help message: bash genome_profiler --help

By default, GenomeProfiler will save its output to ./output_GenomeProfiler.

Semantic Versioning

This repository adheres to Semantic Versioning 2.0.0: https://semver.org/.

Acknowledgements

• Benjamin Alford (Ssolar5): Packaging for distribution, command-line interface, documentation, cleanup.