> 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/illumina-trupath-genome/sequencing-run-setup/instrument-run-setup.md).

# Prerequisites

## NovaSeq X Instrument Software Update

Illumina TruPath Genome is currently supported on [**NovaSeq X Sequencing Systems**](https://www.illumina.com/systems/sequencing-platforms/novaseq-x-plus.html). Ensure that the NovaSeq X Instrument has been upgraded to [**v1.4 Software**](https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/novaseq-x-series/200079828_00_NovaSeq_X_Series_1_4_0_Release_Notes.pdf) prior to starting any TruPath sequencing workflow. The Illumina TruPath Genome C2 (C2, 2 Samples) and C8 (C8, 8 Samples) Flow Cells are only compatible with the NovaSeq X v1.4 software.

Illumina TruPath Genome currently does not support the following settings:

* Custom Primers
* Custom Recipe
* Indexing

NovaSeq X v1.4 Software supports cloud DRAGEN Germline planned runs from BaseSpace Sequence Hub (BSSH). Ensure that the planned run from BSSH has correctly been configured with the DRAGEN Germline 4.5.2 application for use with the Illumina TruPath Genome Flow Cells.

For more information on the NovaSeq X v1.4 Software, [please refer to this link here.](https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/novaseq-x-series/200079828_00_NovaSeq_X_Series_1_4_0_Release_Notes.pdf)

## Cloud Subscription

A cloud account with a valid subscription is required for running analyses in Illumina cloud. For information on registering your BaseSpace Sequence Hub or Illumina Connected Analytics account, [refer to Software Registration page.](https://help.connected.illumina.com/account-management/rg-registration)


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