> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/library-preparation/general/library-preparation-general-reference_material-list/000005773.md).

# Information and protocol for the Illumina Fungal Metagenomics Sequencing workflow

The Illumina Fungal Metagenomics Sequencing demonstrated protocol is a two-step PCR workflow that amplifies the ITS1 region from samples for metabarcoding studies.

The protocol is available on the page, [here](https://support.illumina.com/downloads/fungal-metagenomic-sequencing-demonstrated-protocol-1000000064940.html).

Compatible index primer kits are those listed under the "Index adapters" section within the "Order" tab on the Nextera XT product page, [here](https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/nextera-xt-dna.html). (**Note**: the Illumina Fungal Metagenomics protocol does not use the Nextera XT library preparation kit, this link is only to reference compatible index primer kits.)

For more information, see the application note [Fungal sequencing and classification with the ITS Metagenomics Protocol](https://www.illumina.com/content/dam/illumina-marketing/documents/products/appnotes/its-metagenomics-app-note-1270-2018-001-web.pdf).

\
\
\ <br>

|                                                                                                                                                                                                                                                                                                                                                                              |
| :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *For any feedback or questions regarding this article (Illumina Knowledge Article #5773), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000005773%20-%20Library%20Preparation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


---

# 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://knowledge.illumina.com/library-preparation/general/library-preparation-general-reference_material-list/000005773.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.