> For the complete documentation index, see [llms.txt](https://help.bioinsight.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.bioinsight.illumina.com/illumina-trupath-genome/additional-information/faqs.md).

# FAQs

This page describes Frequently Asked Questions (FAQs) related to Illumina TruPath Genome Software.

* ***Can any Illumina sequencing data be analyzed with TruPath Genome?***
  * No, Illumina TruPath Genome analysis software via DRAGEN Germline must be used with sequencing data generated with the Illumina TruPath Genome assay. Using non-TruPath data or regular Illumina SBS data inputs will lead to analysis failure.
* ***What type of analysis is supported?***
  * Only DRAGEN Germline analysis is supported at this time. Please refer to the DRAGEN User Guide [linked here](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-trupath-pipeline.md) for additional information on supported analyses.
* ***What happens if I analyze standard short-read data with the DRAGEN Germline pipeline?***
  * Analyzing short-read data with the DRAGEN Germline pipeline with proximity mode enabled will lead to analysis failure. The DRAGEN Germline pipeline with proximity mode enabled must be used with TruPath inputs only.
* ***What metrics should be assessed to understand assay performance?***
  * Key Metrics that describe if the assay performed well include NG50, Template Length, and Proximity Coverage. These metrics are output in the DRAGEN Reports for each analysis. For more information on DRAGEN Reports, visit this link here. For more information on the assay itself and related metrics, visit this link here.
* ***Is Illumina TruPath Genome compatible with ICM?***
  * Currently[ Illumina Connected Multiomics (ICM)](https://www.illumina.com/products/by-type/informatics-products/connected-multiomics.html) does not support analysis results from the Illumina TruPath Genome.
* ***Is Emedgene (EMG) compatible with TruPath DRAGEN outputs?***
  * Yes, [Emedgene](https://help.emg.illumina.com/release-notes/workbench-and-pipeline-updates) is compatible with TruPath DRAGEN outputs. Results from secondary analysis may be ingested automatically similar to any other workflow. For additional information on Emedgene and release notes, please visit the Emedgene User Guide[ linked here](https://help.emg.illumina.com/).
* ***Where is the data visualized?***
  * Depending on which output files desired for visualization, secondary analysis outputs may be visualized via Genome Viewer, IGV, Dragen Reports or HiGlass. Please see the child pages under [Data Visualizations and Analysis](/illumina-trupath-genome/data-visualizations-and-analysis/visualize-data-in-platform-core.md) for further details.


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation by asking a question.

Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters:

```
GET https://help.bioinsight.illumina.com/illumina-trupath-genome/additional-information/faqs.md?ask=<question>&goal=<user_goal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.