Platform Core Manual Launch

How to Launch a Manual Analysis

1. Create a Project: A project can be specific for the DRAGEN StrataMap pipeline, or it can contain multiple pipelines and/or tools. For information on creating projects, refer to the Projects section in Illumina BioInsights Platform Core help.

Core standard storage is used by default as soon as the project is saved. To connect a different storage source, set it up before creating your project. For details and options, refer to the Storage section in Illumina BioInsights Platform Core help.

1. Upload the sequencing data: For information on viewing and uploading data, refer to the Data section in Illumina BioInsights Platform Core help.
2. Start Analysis: In the project, navigate to Pipelines, select the DRAGEN StrataMap Pipeline, and then select "Start analysis". Set up the new analysis by configuring the parameters listed in the table below. When the required files are complete, start the analysis.
3. Review Results: After analysis is complete, navigate to results in the configured output location.

Please see the Illumina Support Shorts for guidance on how to set up and run DRAGEN StrataMap analysis on Core.

Analysis Parameters on Core

To launch an analysis via the Core user interface, configure a DRAGEN StrataMap pipeline analysis with the parameters described below. Parameters are grouped into sections in the Core UI.

Data Inputs

Parameter Name	Description
Run Folder(s)	The run folder(s) containing the files to analyze. BaseSpace defaults to saving sequencing runs into the ilmn-runs folder.
Samplesheet	Select a sample sheet in CSV format for the analysis.
Genome	Select Human, Mouse, or custom genomes in tar.gz format. See here for more information
Image Files	Select the registered OME-TIFF image files exported from ISIT for analysis. Image files must align with the Samplesheet.
Analysis Config Path	(Optional) Select an analysis configuration JSON file to set additional analysis parameters. See the user guide for available options and configuration details.
External Segmentation Image Files	(Optional) Use a cell segmentation file generated outside of the pipeline. See this page for more details. IMPORTANT: Files MUST follow the name format "{SAMPLE_ID}_cell_segmentation_mask.tif" or "{SAMPLE_ID}_nuclei_segmentation_mask.tif". Any deviation will cause the workflow to fail.

General Parameters (all optional)

Parameter Name	Description
Slide ID	Enter only if not included in the sample sheet. Sample sheets generated using Run Planner already contain the Slide ID. The ID must be found on the slide and match exactly for successful analysis.
Run Name	Provide a run name to use in the DRAGEN report and run-level metric files. If not provided, the run name will be the date and time of the run.
Compute Resource Size	Dynamic is recommended and will automatically allocate computing resources based on tissue area and flow cell type. Only adjust if troubleshooting — manually select from predefined Medium, Large, or XLarge configurations. Default: Dynamic.

Alignment Parameters (all optional)

Parameters controlling read alignment behavior. Additional DRAGEN alignment settings can be configured via the Analysis Config file. See the user guide for available options and configuration details.

Parameter Name	Description
Output BAM	none produces no output; bam outputs a BAM file. Note: generating BAM alignments will increase compute time and cost. Default: none.
Include Intronic Reads	By default, reads mapping to intronic regions are filtered out. Enable to include intronic reads in the analysis for capturing unspliced transcripts. See Exonic and Intronic Alignments for details. Default: False.
Use only uniquely aligned reads	When enabled, only reads that uniquely align to the genome are used for analysis; multimapping reads are excluded. By default, multimappers are included by prioritizing alignments to protein-coding genes over non-protein coding genes. See Multimapping for details. Default: False.

Cell Segmentation Parameters (all optional)

Parameter Name	Description
Output Nuclei Binned Results	Enable to include analysis on nuclei-binned data. Note: full analysis will run on nuclei-binned data, increasing compute time and the size of the output folder. See Cell and Grid Binning for background on binning. Default: False.
Cell Boundary Expansion Distance	Sets the distance used to expand the nucleus boundary to determine the cell boundary. See Cell Segmentation for details on how expansion works. The default and recommended setting is 5µm.

Tertiary Analysis (all optional)

Parameter Name	Description
Grid Bin Size	Enter a colon-delimited list of integers to submit additional grid bin sizes in addition to the default of 10µm. Analysis will run on each size, increasing compute time and cost. We do not recommend 3µm or smaller bin sizes. See Grid Binning for details. Default: 10µm.
Skip Tertiary	Skip PCA, UMAP, and clustering analysis steps to shorten runtime. See Tertiary Analysis for the steps that are skipped. Default: False.

Core-Specific Options

Parameter Name	Description
User Reference	The analysis run name.
User Tags	Text labels to help index the analysis.
Notify me when task is completed	(Optional) Receive an email notification when analysis is complete.
Output Folder	The path to the analysis output folder. The default path is the Analyses output folder.
Logs Folder	The path to the analysis log folder. The default path is the Logs output folder.
Subscription	Select the billing account associated with the analysis.
Storage Size	(Optional) Storage Size defaults to the maximum size required to complete analysis. For smaller analyses, a smaller storage size may be selected. 1-2 S4 or 1 25B - Large 3-4 S4 or 2-3 25B - X-Large Anything bigger - 2X-Large

For information about using pipelines, refer to Illumina Connected Analytics support site page.

Imageless Analysis on Core

For workflows without microscopy images, the DRAGEN StrataMap uses the SampleLocator feature to automatically detect sample regions. To run an imageless analysis, use the Imageless DRAGEN StrataMap pipeline provided in the DRAGEN StrataMap Bundle.

How Imageless Mode Works

SampleLocator analyzes sequencing data against the map file to automatically identify and segment tissue regions without requiring microscopy images.

Data Transfer to Whitelisted Domain and Workgroup

If data is streamed to the incorrect domain (e.g. public or non-whitelisted domain) and is inaccessible in Core, use the following instructions to transfer data to the correct, whitelisted private domain and workgroup using the BaseSpace Sequence Hub command line interface (BSSH CLI) tool.

These instructions will require you to perform the BSSH CLI tool installation and have your browser open to the intended domain and workgroup while you use a terminal to authenticate the Workgroup.

Note: Items that are [bracketed] require user input.

1. Install the BSSH CLI tool onto the device where runs are saved locally according to the instructions found here: BSSH CLI Installation Instructions
2. In a browser, enter your private BSSH domain URL and log in.

   1. example: https://[private domain name].basespace.illumina.com/dashboard
3. Select the whitelisted Workgroup you intend to use and leave your browser open while you move to the next step.
4. Open a terminal and enter the following commands to authenticate your whitelisted Workgroup:

   1. Authenticate

      bs auth -c [private domain name] --api-server https://api.basespace.illumina.com
   2. Confirm authentication

      bs -c [private domain name] whoami
   3. If authenticated, the result should look like this with the Workgroup listed under "Name":

      INSERT SCREENSHOT HERE
5. Use the following command to send run data to your authenticated Workgroup:

   [location of BSSH CLI] --config [private domain name] run upload --instrument=[NovaSeqX] --name=[run name] --retry [location of run]