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rambaut committed Aug 26, 2024
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content="**Overview:** This document walks-through how to install and run a bioinformatics pipeline for analysing Illumina data generated from the ARTIC amplicon protocol within the ONT EPI2ME desktop software."
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## Background

Nextflow Pipeline created by:
## Credits / Acknowledgements

This pipeline is based on the [BCCDC-PHL/ncov2019-artic-nf](https://github.com/BCCDC-PHL/ncov2019-artic-nf) pipeline, which is a fork of the [connor-lab/ncov2019-artic-nf](https://github.com/connor-lab/ncov2019-artic-nf) pipeline. It has been modified here to support analysis of monkeypox virus. This pipeline is possible due to the ongoing efforts of many people developing and maintaining bioinformatics software. For a complete list of acknowledgments please see the documentation on the pipeline Github repository: [https://github.com/artic-network/artic-mpxv-nf](https://github.com/artic-network/artic-mpxv-illumina-nf/blob/master/README.md)

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## Using the ARTIC MPXV analysis pipeline in EPI2ME
<br/>

**Requirements:**

* A working installation of EPI2ME. For instructions for installing EPI2ME, [see this document](/mpxv/mpxv-epi2me-setup.html).
* Internet access to download the pipeline, and for the first time running it. After that, you should be able to run it offline.
* Details about how the data was generated including the primer scheme used.

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### **Import the workflow**

Open EPI2ME. On the main dashboard select “View workflows”.
Open EPI2ME. On the main dashboard select “View workflows”:

<img width="500" src="/assets/images/mpxv/illumina-sop/screenshot_1.png">

Then select “Import workflow”.
Then select “Import Workflow”:

<img width="500" src="/assets/images/mpxv/illumina-sop/screenshot_2.png">

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