# Introduction

## Illumina TruPath Genome Software

Illumina TruPath Genome Software delivers a comprehensive whole-genome sequencing solution by integrating NovaSeq X sequencing, DRAGEN secondary analysis, and Emedgene interpretation all within the Illumina software ecosystem.

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## Pre-Sequencing

Illumina TruPath Genome C2 and C8 Flow Cells are supported via the NovaSeq X Sequencing Systems. Sequencing must be performed on the [NovaSeq X Instrument Series](https://www.illumina.com/systems/sequencing-platforms/novaseq-x-plus.html) using the [1.4 Software Package.](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)

Secondary analysis via DRAGEN Germline may be performed via the following:

* In the Cloud, via BaseSpace Sequence Hub (BSSH) Run Planning via Autolaunch or in Illumina Connected Analytics (ICA). A cloud account with a valid subscription is required for running analysis via BSSH or ICA. For information on registering for a BaseSpace Sequence Hub or Illumina Connected Analytics account, refer to the [Software Registration page](https://help.connected.illumina.com/account-management/rg-registration)
* On-Prem Server, via DRAGEN Server. Note that Illumina TruPath Genome Software requires a v4 DRAGEN Server for on-prem analyses. For more information on v4 DRAGEN Servers, please refer to [DRAGEN 4.5 User Guide](https://help.dragen.illumina.com/dragen-v4.5-trupath)

## Secondary Analysis

DRAGEN Germline v4.5 supports secondary analysis of TruPath data; analysis may be performed on-premise via local DRAGEN server or in the cloud (BaseSpace Autolaunch or ICA). For more information on DRAGEN Secondary Analysis, please refer to [DRAGEN 4.5 User Guide](https://help.dragen.illumina.com/dragen-v4.5-trupath)

DRAGEN Germline v4.5 currently supports Illumina TruPath Genome, and can be run with different variant calling configurations:

* Human Copy Number Variant and Structural Variant Calling, includes filtering via colocation
* Human Small Variant Calling including Multi-Region Joint Detection (MRJD) calling
* Human No Variant Calling, Map / Align with enhanced phasing capabilities

## Data Visualization

TruPath data provides novel variant calling results which may be visualized using third-party tools such as IGV and HiGlass. DRAGEN Reports also offers novel visualizations for DRAGEN's Multi-Region Joint Detection (MRJD) calling. Refer to the child pages in the "Data Visualization and Analysis" section.

## Interpretation

Tertiary analysis and interpretation may be performed in Emedgene (EMG), with TruPath secondary analysis outputs ingestible by Emedgene. For more information on EMG v40 release, [visit this link here.](https://help.emg.illumina.com/release-notes/workbench-and-pipeline-updates)

## Additional References

For guidance on the assay workflow, please refer to the library prep documentation:\
[<mark style="color:$primary;">Illumina TruPath Genome Assay Guidance</mark>](https://support-docs.illumina.com/LP/TrupathGenome/Content/LP/FrontPages/TruPathGenome.htm)

For additional information on the DRAGEN Germline pipeline, please refer to the DRAGEN documentation: [DRAGEN 4.5 User Guide](https://help.dragen.illumina.com/dragen-v4.5-trupath)

For data associated with the assay, including sample and coverage recommendations, please review the [Illumina TruPath Genome Data Sheet](https://support.illumina.com/content/dam/illumina/gcs/assembled-assets/marketing-literature/trupath-genome-data-sheet-m-gl-03931/trupath-genome-data-sheet-m-gl-03931.pdf) and the [Illumina TruPath Genome Tech Note](https://support.illumina.com/content/dam/illumina/gcs/assembled-assets/marketing-literature/trupath-genome-sample-info-tech-note-m-gl-03932/trupath-genome-sample-info-tech-note-m-gl-03932.pdf)

For the DRAGEN Software Installer for On-Prem customers, [visit the link here.](https://support.illumina.com/downloads/trupath-genome-software.html)

For Illumina TruPath Genome Support, [visit this link here.](https://support.illumina.com/sequencing/sequencing_kits/illumina-trupath-genome.html)