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.
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 |
|---|---|---|---|---|
| fastp | 0.23.2+galaxy0 |
iuc |
10 (2022-02-03) | fastp-10:65b93b623c77 |
| fastp_json_to_tabular | 0.1.0 |
public-health-bioinformatics |
0 (2022-03-10) | fastp_json_to_tabular-0:091a2fb2e7ad |
| tbprofiler | 4.1.1+galaxy0 |
iuc |
14 (2022-03-16) | tbprofiler-14:ac8250086ac3 |
| tbprofiler_json_to_tabular | 0.1.0+galaxy2 |
public-health-bioinformatics |
0 (2023-09-19) | tbprofiler_json_to_tabular-0:3e0d5ceeeb0f |
Please download the provided irida-plugin-tbprofiler-[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 >= 21.01. Please see the IRIDA documentation for more details.
The plugin should now show up in the Analyses > Pipelines section of IRIDA.
You should be able to run a pipeline with this plugin and get analysis results. The results include a TBProfiler report listing detailed strain typing and drug resistance information, a JSON-format TBProfiler result file, a vcf file containing variant information and a bam format alignment.
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 |
|---|---|
| tbprofiler/percent_reads_mapped | Percentage of reads mapped against the reference sequence (H37Rv) |
| tbprofiler/resistance_type | Resistance type (MDR/XDR) |
| tbprofiler/main_lineage | Main lineage |
| tbprofiler/sub_lineage | Sub-lineage |
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.
To install IRIDA to your local Maven repository please do the following:
- Clone the IRIDA project
git clone https://github.com/phac-nml/irida.git
cd irida- Checkout appropriate version of IRIDA
git checkout 21.01- Install IRIDA to local repository
mvn clean install -DskipTestsOnce you've installed IRIDA as a dependency, you can proceed to building this plugin. Please run the following commands:
cd irida-plugin-tbprofiler
mvn clean packageOnce complete, you should end up with a file target/irida-plugin-tbprofiler-<VERSION>.jar which can be installed as a plugin to IRIDA.
The following dependencies are required in order to make use of this plugin.