ICA Cloud App

Prerequisites

To run analyses on Illumina Connected Analytics (ICA), you need:

• An ICA account with a valid subscription

• A project configured for the DRAGEN Solid WGS Tumor Normal Pipeline

For general ICA documentation, refer to the Illumina Connected Analytics Help.

Launching Analysis

Follow these steps to launch a DRAGEN Solid WGS Tumor Normal analysis on ICA:

1. Create a Project

Create a new ICA Project (or use an existing one). The Project can be dedicated to the DRAGEN Solid WGS Tumor Normal v4.4.4 Pipeline or contain multiple pipelines and tools.

📖 For detailed instructions, see Projects in the ICA documentation.

Note: ICA standard storage is used by default when the Project is saved. To use a different storage source, configure it before creating your Project. See Storage for details.

2. Add Bundle to Project

Edit the Project and add the bundle titled "Solid WGS TN v4.4.4 (XX)", where XX is a 2-letter region code for your analysis location. Adding the Bundle automatically provisions:

• The DRAGEN Solid WGS TN Pipeline

• Associated reference files and resources

• Demo data in the Demo_Data folder

📖 For more information, see Bundles in the ICA documentation.

3. Upload Sequencing Data

Upload your sequencing data (FASTQ, BAM, CRAM, or BCL files) to the Project.

📖 For upload instructions, see Data in the ICA documentation.

4. Configure and Start Analysis

1. Navigate to Pipelines in your Project

2. Select the Solid WGS TN v4_4_4_x Pipeline

3. Click "Start New Analysis"

4. Configure the parameters listed in the Analysis Parameters section below

5. Click Start to launch the analysis

5. Download Results

After analysis completion, navigate to the configured output folder to access and download your results.

Analysis Parameters

To launch an analysis via the ICA user interface, configure the DRAGEN Solid WGS Tumor Normal pipeline with the following parameters:

Parameter Name	Description
User Reference	The analysis run name.
User Tags	Text labels to help index the analysis.
Notify me when task is completed	Option to receive an email notification when analysis is complete.
Output Folder	The path to the analysis output folder. The default path is the project output folder.
Entitlement Bundle	Automatically populated from the project details.
Samplesheet	Select a sample sheet in CSV format for the analysis. Note: Sample Sheet selection is optional if starting from a run folder, and required when submitting a FASTQ folder.
Input Directory	The run folder or FASTQ folder that contains files to analyze.
Input Type	Select input type for analysis. Options include: bcl, fastq, bam, cram.
Sample or Pair IDs	Optional subset of Sample IDs or Pair IDs to analyze.
Reference Genome	Select the reference genome. hs37d5_chr is the hg19 reference genome with Chromosome Y PAR masked. It includes the NC_012920 mitochondria genome. The contigs have the chr prefix added, but without the native alternate loci names.
Enable Ora Compression	Enable Ora Compression (True or False). Only applicable when Input Type is bcl.
Enable Post Processing	Enable Post Processing (True or False) to run custom scripts at the end of pipeline.
Storage Size	The storage size to allocate for the analysis. The default and recommended value is Large.
Custom Parameters Config File	Optional. Select Custom Parameters Config File that overrides default config.
Custom Resources Directory	Optional. Select Custom Resources Directory to use with Custom Parameters Config File.
CAUTION - This parameter ...	Optional. This configuration only applies to auto-launch DRAGEN Solid WGS Tumor Normal analysis from FASTQs after BCL conversion. Do not set this parameter when starting analysis from the ICA UI.

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For more information about using ICA and launching pipeline analyses, refer to the Illumina Connected Analytics support page.