ONT epi2me sop

_resources/mpxv/mpxv-ont-epi2me-sop.md

@@ -0,0 +1,100 @@
+---
+title: "Using the ARTIC MPXV ONT pipeline | EPI2ME"
+keywords: protocol
+layout: document
+last_updated: 2024-08-22
+tags: [protocol]
+summary:
+permalink: /mpxv/mpxv-ont-epi2me-sop.html
+folder: mpxv
+title_text: "Running the ARTIC MPXV analysis pipeline for nanopore data using EPI2ME"
+subtitle_text: "ARTIC nanopore protocol | bioinformatics"
+document_name: "ARTIC-MPXV-nanopore-Epi2Me-SOP"
+version: v1.0
+creation_date: 2024-08-22
+revision_date: 
+forked_from: 
+author: Lauren Lansdowne
+citation: 
+nav_menu: false
+show_tile: false
+category: mpxv-epi2me
+---
+
+{% include callout.html
+type='default'
+content='**Overview:** 
+'
+%}
+
+## Using the ARTIC MPXV ONT pipeline in EPI2ME
+
+## ---
+
+**Requirements:**
+
+* EPI2ME already installed (see separate document “Laptop Setup Instructions”)
+* Internet access to download the pipeline, and for the first time running it. After that, you should be able to run it offline
+
+---
+
+### **Import the workflow**
+
+Open EPI2ME. On the main dashboard select “View workflows”.
+
+<img width="500" src="/assets/images/mpxv/ont-sop/screenshot_1.png">
+
+Then select “Import workflow”.
+
+<img width="500" src="/assets/images/mpxv/ont-sop/screenshot_2.png">
+
+A pop-up window will appear where you can enter the GitHub URL. Enter the URL and click “Download” ([https://github.com/artic-network/artic-mpxv-nf](https://github.com/BioWilko/artic-mpxv-nf)):
+
+<img width="500" src="/assets/images/mpxv/ont-sop/screenshot_3.png">
+
+Once it has downloaded, it will be ready in the Available Workflows tab. Select it and you will be taken to a landing page for this workflow.
+
+### **Running the workflow**
+
+From the workflow landing page, click “Run this workflow”.
+
+<img width="500" src="/assets/images/mpxv/ont-sop/screenshot_4.png">
+
+Then select “Run on your computer” and click “Continue”.
+
+<img width="500" src="/assets/images/mpxv/ont-sop/screenshot_5.png">
+
+It will then ask you to select your fastq folders. Select the ones you want and continue.  
+
+<img width="500" src="/assets/images/mpxv/ont-sop/screenshot_6.png">
+
+Go to the Primer Scheme Selection tab and **make sure that the primer scheme matches the one you used**. If your scheme is not listed, you can use the “Custom scheme” section to provide the full path to the directory containing your appropriately named scheme bed and fasta files; \<SCHEME\_NAME\>.bed and \<SCHEME\_NAME\>.fasta.
+
+<img width="500" src="/assets/images/mpxv/ont-sop/screenshot_7.png">
+
+Finally click “Launch workflow”. It will then start running. The runtime will depend on the size of your files and the speed of your computer, but 10-30 minutes is common. While it is running you will see a series of progress bars, and at the top a blue ‘Running’ icon. This will change to green and ‘Complete’ when it has finished.
+
+<img width="500" src="/assets/images/mpxv/ont-sop/screenshot_8.png">
+
+When it has finished you will have a collection of outputs for both consensus and individual barcodes.
+
+## Advanced Options
+
+### **Changing the pipeline version**
+
+If you need to use a previous or a development version of the pipeline, this can be selected from the workflow landing page.
+
+<img width="500" src="/assets/images/mpxv/ont-sop/screenshot_9a.png">
+<img width="500" src="/assets/images/mpxv/ont-sop/screenshot_9b.png">
+
+### **Changing the basecaller**
+
+Medaka runs within the pipeline to call variants between the reads provided and the reference. It will try to auto-select. If it is unable to auto-select (for example if your data was basecalled with a version of MinKNOW which is no longer supported) you may need to choose an option from this drop down list of available models in “Advance Options” (scroll down).
+
+<img width="500" src="/assets/images/mpxv/ont-sop/screenshot_10.png">
+
+**We recommend you use a supported version of MinKNOW**. As a work around, you should select an option from this list of models which matches the flowcell chemistry and sequencing speed.
+
+{% include wellcome-trust.html %}
+
+<div class="pagebreak"> </div>