Introduction

Illumina 5-Base DNA Prep Software

Welcome to the Documentation for the Illumina 5-Base DNA Prep Analysis Software.

For guidance on the assay workflow, please refer to the library prep documentation at https://support.illumina.com/sequencing/sequencing_kits/illumina-5-base-dna-prep/documentation.html or https://support.illumina.com/sequencing/sequencing_kits/illumina-5-base-dna-prep-enrichment/documentation.html.

For additional information on the DRAGEN pipeline, please refer to the DRAGEN documentation at https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-methylation-pipeline/dragen-5base-pipeline.

Pre-sequencing

Configure your instrument to send runs to BaseSpace Sequence Hub (BSSH) Run Monitoring and Storage. Prepare your sample sheet for sequencing and secondary analysis using the BSSH Run Planning tool with the specifications listed in the child pages.

Sequencing

Sequencing can be done on either a NovaSeq X or NovaSeq 6000. For each system, the data must be converted from BCLs to FASTQs, which can be performed locally or in the cloud (BSSH or ICA). The biosamples (.fastq files) can then be used for secondary analysis.

Secondary Analysis

Secondary analysis may be performed on a local DRAGEN server or in the cloud (BSSH or ICA).

Samples may be downsampled; for more information about downsampling, please see https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-dna-pipeline/downsampling.

There are 3 apps that support this product, and each can be run with different levels of variant calling:

• DRAGEN Germline v4.4.6

  • Human CNV + SV Calling

  • Human Small Variant Calling

  • Human No Variant Calling (Methylation Only)

  • Non-Human No Variant Calling (Methylation Only)

• DRAGEN Somatic v4.4.6

  • Tumor-Only Mode

  • Tumor-Normal Mode

• DRAGEN Enrichment v4.4.6

  • Somatic High Coverage

  • Somatic Medium Coverage

  • Somatic Low Coverage

  • Non-Human Enrichment Germline

Tertiary analysis may be performed in Illumina Connected Multiomics (ICM).