This repository contains a list of pipelines in IRIDA available as plugins.
The IRIDA group does not maintain these plugins so any questions or concerns should be directed to the plugin's developers.
To install each of these plugins, please download the appopriate JAR file from the Release link and copy to the directory /etc/irida/plugins/ on a machine running IRIDA. Then, re-start IRIDA and you should see the pipeline appear in your list of pipelines.
Please see the IRIDA Pipeline Plugin documentation for more details.
| Name | Repository | Description | Release |
|---|---|---|---|
| Example Plugin | https://github.com/phac-nml/irida-plugin-example | An Example plugin to be used as a template for developing IRIDA pipeline plugins. |  |
| AMR Detection | https://github.com/phac-nml/irida-plugin-amr-detection | A pipeline for the detection of antimicrobial resistance genes in bacterial isolates. |  |
| ECTYPER | https://github.com/phac-nml/irida-plugin-ectyper | A pipeline to in silico serotype E.coli isolates |  |
| MLST | https://github.com/public-health-bioinformatics/irida-plugin-mlst | A pipeline for traditional MLST using PubMLST schemas. |  |
| QI-TAXON | https://github.com/quadram-institute-bioscience/irida-plugin-qi-taxon | A pipeline for read based taxon classification. |  |
| QI-PHYLO | https://github.com/quadram-institute-bioscience/irida-plugin-qi-phylo | A pipeline for rFast phylogeny pipeline (Snippy, IQTree) |  |
| Species Abundance | https://github.com/public-health-bioinformatics/irida-plugin-species-abundance | Estimate relative species abundance with Kraken2 & bracken |  |
| Resistance Screen | https://github.com/public-health-bioinformatics/irida-plugin-resistance-screen | Detect presence of specific resistance genes |  |
| TETyper | https://github.com/public-health-bioinformatics/irida-plugin-tetyper | Determine sequence types for specific transposable elements |  |
| Snippy Single | https://github.com/public-health-bioinformatics/irida-plugin-snippy-single | Variant calling against a reference genome for a single isolate |  |
| MiCall-Lite | https://github.com/public-health-bioinformatics/irida-plugin-micall-lite | Human RNA Virus Genotyping |  |
| Plasmid Screen | https://github.com/public-health-bioinformatics/irida-plugin-plasmid-screen | Locate resistance genes on plasmids |  |
| TBProfiler | https://github.com/public-health-bioinformatics/irida-plugin-tbprofiler | Identify lineage and drug resistance variants in M. tuberculosis |  |
| Snippy Phylogenomics | https://github.com/public-health-bioinformatics/irida-plugin-snippy-phylogenomics | Variant calling and core genome alignment with Snippy, phylogenetic tree reconstruction with IQTREE |  |
| SISTR | https://github.com/phac-nml/irida-plugin-sistr | The Salmonella In Silico Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies |  |
| COMBAT-TB: M. tuberculosis sample report | https://github.com/COMBAT-TB/irida-plugin-tb-sample-report | Report on variants and drug resistance in M. tuberculosis samples using TBProfiler and the COMBAT-TB eXplorer |  |
| COMBAT-TB: M. tuberculosis phylogeny | https://github.com/COMBAT-TB/irida-plugin-tb-phylogeny | Compute phylogeny from set of M. tuberculosis samples |  |
To develop a new plugin, please refer to the IRIDA Pipeline Plugin documentation in IRIDA and the IRIDA Example Plugin or existing plugins listed above.
We welcome the contribution of any pipelines you have developed for IRIDA. If you wish to include this pipeline in the list, please submit a Pull Request to this repository which adds a new entry to the table in the Plugins section. This will be in the format of:
| [NAME] | [REPOSITORY/URL] | [DESCRIPTION] | [RELEASE] |
The [RELEASE] could be a direct link to your GitHub releases page (e.g., https://github.com/phac-nml/irida-plugin-amr-detection/releases), a link to the appropriate JAR file, or if you wish to make use of a badge for your release/repository, you can refer to https://shields.io/category/version.
Text in this repository is licensed under the Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/ license. Licenses for each IRIDA plugin are specific to each plugin and should be available from the respective code repositories.