How to use the DRAGEN TSO500 v1.1/DRAGEN TSO500 ctDNA v1.2 pipelines on ICA using FASTQ files

Like the local versions, the TruSight Oncology 500 (TSO500) pipelines on Illumina Connected Analytics (ICA) can take FASTQ files as input as an alternative to providing the entire run folder as input. If the TSO500 Solid/Liquid samples from a run have already been demultiplexed with BCL Convert (locally or on BaseSpace), use the following steps to run the TSO500 apps with these FASTQ files.

1. Create a project on ICA and link the DRAGEN TSO500 v1.1/ DRAGEN TSO500 ctDNA v1.2 entitled bundle to this project. Information about linking a bundle to a project on ICA is available here.

2. Create a folder containing the FASTQ files. Make sure the folder structure follows this format: ${full_path_to_fastqfolder}/${Sample_ID}/${Sample_ID}_Sample#_Lane#_Read#_001.fastq.gz

File pairs must be kept in the same folder.

--FASTQ Folder

----{Sample ID}

------{Sample ID }_S#_L00#_R1_001.fastq.gz

------{Sample ID }_S#_L00#_R2_001.fastq.gz

1. Upload the FASTQ folder to a project on ICA. Obtain the Project ID from the URL of the project: https://ica.illumina.com/ica/#!projectData/p_{Project ID}/

Folders can either be uploaded using Connectors or using the CLI.

a) Information about creating and using Connectors is available here.

b) Information about uploading folders using the CLI is available here.

Use the following commands to upload a folder using the CLI - icav2 project data upload ${full_path_to_fastqfolder} --project-id {Project ID}

1. For DRAGEN TSO500 ctDNA v1.2 only. Upload the run folder to the project. Use CLI or a service connector to upload the run folder.

Suppose there is a concern about uploading the entire run folder (due to the size and presence of other libraries in the run). In that case, a minimal run folder consisting of the following files can be created and uploaded:

a) CopyComplete.txt

b) RunParameters.xml

c) RunInfo.xml

1. Upload the Sample Sheet. Templates can be found in the one of the folders that gets added to the project after linking the entitled bundle: /DRAGEN_TSO500_ctDNA_RUO_v1.2_files/resources/sampleSheet or /DRAGEN_TSO500_RUO_v1.1_files/resources/sampleSheet

SampleSheets can be uploaded from the UI or using a Connector/the CLI. Information about uploading a file using the UI is available here.

1. Launch the Pipeline. Go to the Pipelines tab under Flow, select the pipeline and click on 'Start New Analysis'.

• Give the pipeline analysis a name (User Reference).

• Select the uploaded SampleSheet and the FASTQ folder.

• (For DRAGEN TSO500 ctDNA v1.2 only) Select the Run Folder.

• Select the Resource Folder Path - select the resources folder from /DRAGEN_TSO500_RUO_v1.1_files or /DRAGEN_TSO500_ctDNA_RUO_v1.2_files (both folders get added after the entitled bundle gets linked).

• (for DRAGEN TSO500 v1.1 only) Select the Hashtable Folder Path - select the ref_hashtable folder from /DRAGEN_TSO500_RUO_v1.1_files

• Set start_from_fastq to true.

• Configure other options such as Output Folder, sample_pair_ids and launch the analysis.

  

For any feedback or questions regarding this article (Illumina Knowledge Article #7098), contact Illumina Technical Support [e-mail].