IRIDA TETyper Pipeline Plugin

This project contains a pipeline implemented as a plugin for the IRIDA bioinformatics analysis system. This can be used to determine the sequence type of specific transposable elements that may be present in bacterial isolates.

Table of Contents

• IRIDA TETyper Pipeline Plugin
• Installation
  • Installing Galaxy Dependencies
  • Installing to IRIDA
• 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
tetyper	1.1	iuc	1 (2020-01-18)	tetyper-1:36093854bfc7

Installing to IRIDA

Please download the provided irida-plugin-tetyper-[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.

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 summary of the TETyper typing results, a .vcf file containing SNPs and a blast report indicating where deletions were detected. A TETyper .log file and a .bam alignment file are also provided.

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
tetyper/type	Transposable element type (accounting for both SNPs and Structural variants). Corresponds to Combined_variant field in TETyper summary output
tetyper/left_flanks	A list of distinct sequences passing quality filters that flank the start position of the reference. If multiple sequences are reported, they are delimited by `
tetyper/right_flanks	A list of distinct sequences passing quality filters that flank the end position of the reference. If multiple sequences are reported, they are delimited by `

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-tetyper

mvn clean package

Once complete, you should end up with a file target/irida-plugin-tetyper-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)