Typing Salmonella data with SISTR

This is a quick tutorial on how to use IRIDA to analyze data with the Salmonella in-silico Typing Resource (SISTR).

Initial Data

The data for this tutorial comes from https://irida.corefacility.ca/downloads/data/irida-sample-data.zip. It is assumed the sequence files in miseq-run-salmonella/ have been uploaded into appropriate samples as described in the Web Upload Tutorial. Before starting this tutorial you should have a project with samples that appear as follows:

tutorial-sistr-samples.png

Adding Samples to the Cart

Before a pipeline can be run a set of samples and sequence read data must be selected and added to the cart. For this tutorial please select the single sample and click the Add to Cart button.

add-to-cart.png

Once the samples have been added to the cart, the samples can be reviewed by clicking on the Cart button at the top.

cart-button.png

Selecting a Pipeline

Once inside the cart, the Select a Pipeline button can be used to select a pipeline to run on the selected samples.

select-a-pipeline.png

From the Select a Pipeline view a number of different pipelines are available.

select-a-pipeline-view.png

For this tutorial, we will select the SISTR Pipeline.

Selecting Parameters

Once the pipeline is selected, the next page provides an overview of all the input files, as well as the option to modify parameters.

sistr-pipeline-page.png

We will use the default parameters. Please use the Ready to Launch? button to start the pipeline.

ready-to-launch-button.png

Once the button is selected you should see a screen showing that your pipeline has been launched.

pipeline-launch.png

Monitoring Pipeline Status

To monitor the status of the launched pipeline, please select the Analysis > Your Analyses menu.

your-analyses-menu.png

The will bring you to a page where you can monitor the status of each launched workflow.

your-analyses-page.png

Clicking the pipeline name SISTRTyping_20170418_AE014613 will bring you to a page for that analysis pipeline. This page will continue to refresh as the pipeline progresses through each stage. It will take a while for the SISTR analysis pipeline to complete.

Viewing the Results

Once the pipeline is complete, you will see the SISTR Typing results within your browser and you will be given the option to download the results of the analysis. For more details on interpreting the results, please see the IRIDA SISTR Documentation.

sistr-results.png

Interpreting the Results

For information on interpreting the SISTR results, please refer to the detailed SISTR Report Documentation.

Viewing Provenance Information

To view the pipeline provenance information, please select the Provenance tab.

sistr-provenance.png

This will display the individual steps of this pipeline and the parameters used at each step.