This tutorial demonstrates major functions of the ICA platform, beginning with setting up a project with instrument run data to prepare to use pipelines, and concluding with viewing pipeline outputs in preparation for eventually ingesting outputs into available modules.
In the following example, we start from an existing ICA project with demultiplexed instrument run data (fastq), use the DRAGEN Germline pipeline, and view output data.
This tutorial assumes the user already has an existing project in ICA. To create a new project, please see instructions in the Projects page.
Additionally, you will need the DRAGEN Demo Bundle linked to your existing ICA project. The DRAGEN Demo Bundle is an an entitled bundle provided by Illumina with all standard ICA subscriptions and includes DRAGEN pipelines, references, and demo data.
For general steps on creating and linking bundles to your project, see the Bundles page. This tutorial explores the DRAGEN Germline Published Pipeline, so we will need to link the DRAGEN Demo Bundle to our existing project.
- Go to your project's
- Click the
- Click the
+button, under LINKED BUNDLES
- Click on the
DRAGEN Demo Bundle, then click the
- There may be multiple versions of DRAGEN Demo Bundles. This tutorial details steps for
DRAGEN Demo Bundle 3.9.5.Steps for other versions after 3.9.5 should be similar.
- Click the
DRAGEN Demo Bundle assets should be available now in your projects
After setting up the project in ICA and linking a bundle, we can run various pipelines.
This example demonstrates how to run the DRAGEN Germline Published Pipeline (version 3.9.5) in your ICA project using the demo data from the linked DRAGEN Demo Bundle.
The required pipeline input assets for this tutorial include:
- Illumina DRAGEN Germline Demo Data folder
- Illumina DRAGEN Enrichment Demo Data folder
- Illumina References folder
- DRAGEN Germline
DRAGEN Germline 3.9.5, and then click
Start New Analysis. Initial set-up details require a
User Reference(pipeline run name meaningful to the user) and an
Entitlement Bundlefrom the drop-down menu under
Running the DRAGEN Germline pipeline uses the following inputs:
- FASTQ files
- Select the FASTQ files in the
Illumina DRAGEN Enrichment Demo Datafolder
- Select a reference genome from the
Illumina Referencesfolder (do not select a methyl-converted reference genome for this tutorial)
- Ie: hg38_altaware_nohla-cnv-anchored.v8.tar (suggested, if enabling CNV analysis)
The DRAGEN Germline Settings to be selected are:
- Enable germline small variant calling: Set to
- Enable SV (structural variant) calling: Set to
- If true, Enable map align output must also be set to
- Enable repeat genotyping: Set to
- Enable map align: Set to
- When using FASTQ files as input, as in this example, set this to
- When using BAM files as input, set to
trueto realign reads in input BAMs; set to
falseto keep alignments in input BAM files.
- Enable CNV calling: Set to
- Enabling Copy Number Variant calling requires one of the following:
- Enable CNV self normalization is set to
- A panel of normals (PON) is provided in the Input Files
- Output format: Set to
- Other available options for alignments output are BAM and SAM format.
- Enable CNV self-normalization: Set to
- Required if Enable CNV calling is set to
trueand no panel of normals (PON) is provided in the Input Files.
- Enable duplicate marking: Set to
- Emit Ref Confidence: Set to
GVCFto enable banded gVCF generation for this example
- To enable base pair resolution in the gVCF, set to
- Additional DRAGEN args: None
- Users can provide additional DRAGEN arguments here (see the DRAGEN user guide for examples), but we will leave this blank for this example run.
- Sample sex: Leave blank
- Users may specific the sex of the sample here if known, but the user will omit this setting for this example run.
- Enable HLA: Set to
trueto enable HLA typing
- Enable map align output: Set to
- The format for alignment output was selected previously in the "Output format setting" above
- Use the default resources settings:
- Storage size: Set to
- FPGA Medium Tier: Set to
- FPGA Medium Resources: Set to
Once all parameters have been set, click
Users can monitor the status of analysis pipeline runs from the
Runspage in their project.
Possible statuses include:
Click the refresh button in upper left corner of the ICA environment page to see updated status.
Click on the run to view more information about it. The various tabs (
Logs) under a given run provide additonal context regarding the status of the completed run. (Note:
Detailsare only available in ICA for graphical CWL pipelines, of which DRAGEN Germline is one.)
If the user encounters a failed run, an error message can be found by expanding the "Error" reporting in the
Analysis run logs can be found on the
Logstab; check the boxes next to the log files to view them in the text viewer. Check the box next to "Show technical steps" to view additional log files.
DRAGEN analysis output folders are found on the project's
Datapage, along with all other data loaded to the project (such as assets from a linked entitled bundle). Output analysis will be grouped into folders, so users can click through the directory structure to explore outputs.
- DRAGEN Support Site: https://support.illumina.com/sequencing/sequencing_software/dragen-bio-it-platform.html
- ICA Pricing: https://help.ica.illumina.com/reference/r-pricing