IRIDA Resistance-Screen Pipeline Plugin

This project contains a pipeline implemented as a plugin for the IRIDA bioinformatics analysis system. This can be used to detect the presence of specific resistance genes in a sample.

Table of Contents

• IRIDA Resistance Screen Pipeline Plugin
• Installation
  • Installing Galaxy Dependencies
  • Installing to IRIDA
  • Setting up your abricate report screening file(s)
• Usage
  • Analysis Results
  • Metadata Table
• Building
  • Installing IRIDA to local Maven repository
  • Building the plugin
• Dependencies

Installation

Installing Galaxy Dependencies

In order to use this pipeline, you will also have to install the following Galaxy tools and data managers within your Galaxy instance. These can be found at:

Name	Version	Owner	Metadata Revision	Galaxy Toolshed Link
shovill	1.0.4	iuc	3 (2018-11-13)	shovill-3:865119fcb694
quast	5.0.2	iuc	5 (2018-12-04)	quast-5:81df4950d65b
abricate	0.9.8	iuc	7 (2019-10-29)	abricate-7:4efdca267d51
screen_abricate_report	0.4.0	public-health-bioinformatics	4 (2020-01-03)	screen_abricate_report-4:22247b1a59d5
data_manager_manual	0.0.2	iuc	5 (2019-10-21)	data_manager_manual-5:744f607fac50

Installing to IRIDA

Please download the provided irida-plugin-resistance-screen-[version].jar from the [releases][] page and copy to your /etc/irida/plugins directory. Now you may start IRIDA and you should see the pipeline appear in your list of pipelines.

Note: This plugin requires you to be running IRIDA version >= 19.01. Please see the IRIDA documentation for more details.

Setting up your abricate report screening file(s)

Abricate report screening files have a simple tabular format, and can be created with Excel, another spreadsheet application, or a plaintext editor. They consist of two columns, with headings gene_name and regex. All fields must be tab-delimited.

gene_name    regex
KPC          ^KPC-\d+$
OXA          ^OXA-\d+$
NDM          ^NDM-\d+$

Preparing the 'abricate_report_screening_files' Tool Data Table in Galaxy

This workflow requires that the abricate report screening files described above are made available via a Galaxy Tool Data Table called abricate_report_screening_files. We recommend that you use the data_manager_manual tool to manage that data table.

Usage

The plugin should now show up in the Analyses > Pipelines section of IRIDA.

Analysis Results

You should be able to run a pipeline with this plugin and get analysis results. The results include a full abricate report, and a screened abricate report that includes only your genes of interest.

Metadata Table

And, you should be able to save and view these results in the IRIDA metadata table. The following fields are written to the IRIDA 'Line List':

Field Name	Description
resistance-screen/<GENE_NAME>/detected	Whether or not GENE_NAME was detected (True/False)
resistance-screen/<GENE_NAME>/alleles	Any allele(s) detected for GENE_NAME. If multiple alleles detected, commma-delimited (eg: KPC-2,KPC-3)

Note: If your abricate report screening file contains many genes, this will result in many columns

Building

Building and packaging this code is accomplished using Apache Maven. However, you will first need to install IRIDA to your local Maven repository. The version of IRIDA you install will have to correspond to the version found in the irida.version.compiletime property in the pom.xml file of this project. Right now, this is IRIDA version 19.01.3.

Installing IRIDA to local Maven repository

To install IRIDA to your local Maven repository please do the following:

1. Clone the IRIDA project

git clone https://github.com/phac-nml/irida.git
cd irida

2. Checkout appropriate version of IRIDA

git checkout 19.01.3

3. Install IRIDA to local repository

mvn clean install -DskipTests

Building the plugin

Once you've installed IRIDA as a dependency, you can proceed to building this plugin. Please run the following commands:

cd irida-plugin-resistance-screen

mvn clean package

Once complete, you should end up with a file target/irida-plugin-resistance-screen-0.1.0-SNAPSHOT.jar which can be installed as a plugin to IRIDA.

Dependencies

The following dependencies are required in order to make use of this plugin.

• IRIDA >= 0.23.0
• Java >= 1.8 and Maven (for building)