Cloud Analysis Auto-launch Settings

Sample Sheet

The orchestration of auto-launched ICA pipelines is driven by information provided in the sequencing run sample sheet. When leveraging BaseSpace Run Planning to plan a run, the sample sheet is automatically generated. The sample sheet may also be attached to the run manually on the sequencer. The following sections are necessary for powering the autolaunch of secondary analysis after the sequencing run completes.

To retreive the most up-to-date sample sheet template for your instrument, generate an example using BaseSpace Run Planning.

Use Run Planning to Export a Sample Sheet

1. Log into your BaseSpace Sequence Hub account.

2. Select the Runs tab, and then select the New Run drop-down.

3. Select Run Planning.

4. In the Run Name field, enter a unique name of your preference to identify the current run. The run name can contain a maximum of 255 alphanumeric characters, spaces, dashes, and underscores.

5. Optional: Enter a description for the run. The run description can contain a maximum of 255 characters.

6. Select your sequencing system as the instrument platform.

7. For Secondary Analysis, Select BaseSpace.

   1. Note that if you have an ICA subscription, this option will read BaseSpace / Illumina Connected Analytics.

8. Optional: Enter the ID for your library tube. The library tube ID is located on the label of your library tube strip.

9. Select Next.

10. Select your analysis application. If only one option is available, it will be selected automatically.

11. Optional: Enter a description for the configuration.

12. Select an existing library prep kit, or add a new custom library prep kit as follows:

    1. Select Add Custom Library Prep Kit under the Library Prep Kit dropdown.

    2. Enter the name, read types, default read cycles, and compatible index adapter kits for your custom library prep kit.

    3. Select Create New Kit.

13. Select an existing index adapter kit, or add a new a custom index kits as follows. If you are using more than one library, the libraries must have the same index read lengths.

    1. Select Add Custom Index Adapter Kit under the Index Adapter Kit dropdown.

    2. Select a template type and enter the kit name, adapter sequences, index strategies, and index sequences. Make sure the second index (i5) adapter sequences are in forward orientation.

    3. Select Create New Kit.

14. If applicable to your application, select a reference genome.

15. Select Next to configure secondary analysis settings. Detailed instructions for each application and version can be found here.

16. Select Next to review the Run and Analysis details.

17. Select Export to save the Sample Sheet to your device.

The FileFormatVersion in the [Header] section must be set to 2 to indicate the sample sheet as v2 format.

[Header],
FileFormatVersion,2

Sample sheets generated using BaseSpace Run Planning may contain additional optional header fields such as RunName, InstrumentPlatform, and IndexOrientation.

Primary Analysis Settings

The primary analysis settings consist of the information used for the on-instrument sequencing and demultiplexing of raw sequencing output data. This includes information about reads, indices, primers, etc.

These sections vary greatly depending on the instrument type used and sequencing configuration. The below examples are used for demonstration purposes only.

[Reads],
Read1Cycles,1
Read2Cycles,1
Index1Cycles,1
Index2Cycles,1

[Sequencing],
CustomRead1Primer,false
CustomRead2Primer,false
CustomIndex1Primer,false
CustomIndex2Primer,false

[BCLConvert_Settings],
SoftwareVersion,0
BarcodeMismatchesIndex1,
BarcodeMismatchesIndex2,
AdapterRead1,
AdapterRead2,
OverrideCycles,

For demultiplexing the raw sequencing output data, the settings for demultiplexing (ie, BCL Convert) are included. The below examples are used for demonstration purposes only.

[BCLConvert_Settings],
Sample_ID,NS001
Index,T
Index2,A
Lane,1

Secondary Analysis Settings

A [Cloud_<pipeline_name>_Settings] and [Cloud_<pipeline_name>_Data] setting are provided for each secondary analysis pipeline to be auto-launched after sequencing. The value used for <pipeline_name> can be any value. It's best practice to refer to the analysis type such as "DragenGermline", "BCLConvert", etc. These sections provide input parameters to the pipelines. The contents of these sections, including the columns, may vary depending on the pipeline used for secondary analysis. The below snippet demonstrates using "DragenGermline" as an example.

[Cloud_DragenGermline_Settings]
SoftwareVersion,4.1.5
MapAlignOutFormat,bam
 
[Cloud_DragenGermline_Data]
Sample_ID,ReferenceGenomeDir,VariantCallingMode
<sample_id>,urn:ilmn:ica:region:<region_guid>:data:<data_guid>#<data_path>,None
<sample_id>,urn:ilmn:ica:region:<region_guid>:data:<data_guid>#<data_path>,None

The [Cloud_Settings] section must be present and include:

1. Cloud_Workflow value set to ica_workflow_1

2. BCLConvert_Pipeline set a valid ICA Uniform Resource Name (URN) for demultiplexing

   1. Note: To find secondary analysis URNs for a specific pipeline, click on the pipeline in the Pipelines section in ICA, and view the Information tab.

3. [Optional] One or more Cloud_<pipeline_code>_Pipeline entries set to a valid ICA URN for secondary analysis.

[Cloud_Settings]
GeneratedVersion,0.0.0
Cloud_Workflow,ica_workflow_1
BCLConvert_Pipeline,urn:ilmn:ica:pipeline:<pipeline_uuid>#<pipeline_code>
Cloud_DragenGermline_Pipeline,urn:ilmn:ica:pipeline:<pipeline_uuid>#<pipeline_code>

The `<pipeline_name>` used in the `[Cloud_<pipeline_name>_Settings]` and `[Cloud_<pipeline_name>_Data]` must exactly match the value used in the `[Cloud_Settings]` section for the `[Cloud_<pipeline_name>_Pipeline]`.