> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/dragen-5-base/additional-information/pre-sequencing-and-sequencing.md).

# Pre-Sequencing and Sequencing

### Pre-Sequencing <a href="#sequencing" id="sequencing"></a>

Configure your instrument to send runs to BaseSpace Sequence Hub (BSSH) Run Monitoring and Storage. Prepare your sample sheet for sequencing and primary analysis (BCL Convert) using the BSSH Run Planning tool with instructions listed under [Sequencing Run Setup](broken://pages/NlX5WPmHglWfe1L8eBZA).

### Sequencing <a href="#sequencing" id="sequencing"></a>

Sequencing can be done on a NovaSeq X, NovaSeq 6000, or NextSeq 2000. 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. For instrument set up instructions, see the [Instrument Domain Setup](broken://pages/gbAIQ65TNTaNuu9fkbZQ) pages.


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