User Guide document needs to be updated for Hash Table Generation

[partha-edico]

The Dragen Hash Table generation Workflow has some differences from other pipelines that require changes to the main Dragen quickstart script so it is not yet supported. It can be added if there is sufficient need for it. In the meantime, the docs need to be updated to provide an alternative method for generating custom hash tables.

[usuyama]

Hi @partha-edico @vsnyc

I'm trying to run a sample job using the sample data:

• NIST7035_TAAGGCGA_L001_R1_001_trimmed.fastq.gz
• NIST7035_TAAGGCGA_L001_R2_001_trimmed.fastq.gz

following the quick guide https://aws-quickstart.s3.amazonaws.com/quickstart-illumina-dragen/doc/dragen-on-the-aws-cloud.pdf

What should I do about the reference data? --ref-dir s3://<bucket/path>

The guide says

The DRAGEN-specific reference hash table directories that are provided by Illumina or that you create from FASTA files

but I'm not sure how to prepare this reference hash table directories.

[partha-edico]

@usuyama Because the HT generation only needs to be runs and re-used across runs it is not currently supported by this Quickstart implementation. You will have to use the DRAGEN AMI to create a Hash Table and upload to S3. An example of how to do this can be found in a Dragen getting started guide, i.e. https://dragen-docs-public.s3.amazonaws.com/DRAGEN+Getting+Started+Guide+v3.5.7.pdf