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artic-network · Aug 23, 2024 · 23259e3 · 23259e3
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diff --git a/_resources/mpxv/mpxv-bioinformatics-sop.md b/_resources/mpxv/mpxv-bioinformatics-sop.md
@@ -8,7 +8,7 @@ permalink: /mpxv/mpxv-bioinformatics-sop.html
 folder: ncov
 title_text: "MPXV Nanopore sequencing bioinformatics protocol"
 subtitle_text: "Nanopore | bioinformatics"
-document_name: "ARTIC-MPXV-bioinformaticsSOP"
+document_name: "ARTIC-MPXV-bioinformatics-SOP"
 version: v1.0.0
 creation_date: 2024-08-20
 forked_from: 
@@ -204,3 +204,15 @@ To put all the consensus sequences in one file called ```my_consensus_genomes.fa
 ```bash
 cat *.consensus.fasta > my_consensus_genomes.fasta
 ```
+
+---
+
+> This document is part of the MPXV sequencing protocol package:
+: [http://artic.network/mpxv](http://artic.network/mpxv)
+
+<br /><br /><br />
+
+{% include wellcome-trust.html %}
+<br />
+
+<div class="pagebreak"> </div>
diff --git a/_resources/mpxv/mpxv-epi2me-setup.md b/_resources/mpxv/mpxv-epi2me-setup.md
@@ -92,9 +92,13 @@ Once it has downloaded, it will be ready in the `Available Workflows` tab. Selec
 ## Running a pipeline
 
 > For instructions on running individual ARTIC pipelines in EPI2ME see the [list of documents here](/mpxv).
-                        
-<br /><br />
+
+> This document is part of the MPXV sequencing protocol package:
+: [http://artic.network/mpxv](http://artic.network/mpxv)
+
+<br /><br /><br />
 
 {% include wellcome-trust.html %}
+<br />
 
 <div class="pagebreak"> </div>
diff --git a/_resources/mpxv/mpxv-ont-bioinformatics-epi2me-sop.md b/_resources/mpxv/mpxv-ont-bioinformatics-epi2me-sop.md
@@ -1,15 +1,15 @@
 ---
-title: "Setting up and using EPI2ME for ARTIC pipelines | EPI2ME"
+title: "Running the ARTIC nanopore bioinformatics pipeline using EPI2ME | bioinformatics"
 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 pipelines using EPI2ME"
+title_text: "Running the ARTIC nanopore bioinformatics pipeline using EPI2ME"
 subtitle_text: "ARTIC pipelines | bioinformatics"
-document_name: "ARTIC-MPXV-EPI2ME-Setup"
+document_name: "ARTIC-MPXV-bioinformatics-EPI2ME-SOP"
 version: v1.0
 creation_date: 2024-08-22
 revision_date: 
@@ -23,53 +23,17 @@ category: mpxv-epi2me
 
 {% include callout.html
 type='default'
-content="**Overview:** This document walks-through how to install and setup Oxford Nanopore Technology's EPI2ME software package so that it can be used to run ARTIC bioinformatics pipelines on a Desktop or Laptop computer without having to use a command-line interface."
+content="**Overview:** This document walks-through how to install and run the ARTIC bioinformatics pipeline in the ONT EPI2ME desktop software."
 %}
 
 **Requirements:**
 
-* The ability to install software on your desktop or laptop. This includes some extra packages like Java and Docker that may require administrator level privileges.   
+* 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 and the base-caller specified within the MinKNOW software.
 
 ---
 
-## Installing the EPI2ME software
-
-EPI2ME is a standard desktop software package available for Windows, Macintosh and Linux operating systems and is used to run 'NextFlow' pipelines in a simple easy-to-use environment without interacting with a command-line. It can be obtained from the EPI2ME website --- [https://labs.epi2me.io]() --- with downloads for each operating system available from the download page:
-
-> [https://labs.epi2me.io/downloads/](https://labs.epi2me.io/downloads/)
-
-Once you have downloaded the appropriate installer for your operating system, install it in the usual way.
-
-## Initial setup of EPI2ME
-
-When you run EPI2ME it will ask if you want to sign-up or sign-in to the Cloud-based service --- you can just click the `Continue without signing in` button.                               
-
-The first time you run EPI2ME it may need to install some additional software. It will guide you through this process.
-
-<img width="500" src="/assets/images/mpxv/epi2me-install/screenshot1.png"> 
-                      
-If you see a panel that says `Additional setup is required` then select it:
-
-<img width="500" src="/assets/images/mpxv/epi2me-install/screenshot2.png"> 
-
-You may need to install the `NextFlow` software and `Java` - in which case click the `Setup` button:
-
-<img width="500" src="/assets/images/mpxv/epi2me-install/screenshot3.png"> 
-
-Then click `Continue ->`. Unless it has already been installed it will next ask you to install the `Docker` software. Click on the link to `Docker Desktop Install` and follow the instructions there to install `Docker`:
-
-<img width="500" src="/assets/images/mpxv/epi2me-install/screenshot3c.png"> 
-
-When it says `Docker is ready`, click `Finish`. The EPI2ME window will now look like this:
-
-<img width="500" src="/assets/images/mpxv/epi2me-install/screenshot4.png"> 
-
-You are now ready to install an analysis pipeline in EPI2ME.
-
-# ---
-
 ## Using an ARTIC MPXV analysis pipeline in EPI2ME
 
 ### **Import the workflow**
@@ -82,7 +46,7 @@ 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)):
+A pop-up window will appear where you can enter the GitHub URL. Enter the URL  (`https://github.com/artic-network/artic-mpxv-nf`) and click “Download”:
 
 <img width="500" src="/assets/images/mpxv/ont-sop/screenshot_3.png">
 
@@ -128,7 +92,16 @@ Medaka runs within the pipeline to call variants between the reads provided and
 <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.
+
+---
+
+## Related documents:
+This document is part of the MPXV sequencing protocol package:
+: [http://artic.network/mpxv](http://artic.network/mpxv)
+
+<br /><br /><br />
 
 {% include wellcome-trust.html %}
+<br />
 
 <div class="pagebreak"> </div>
diff --git a/_resources/mpxv/mpxv-phylogenetics-epi2me-sop.md b/_resources/mpxv/mpxv-phylogenetics-epi2me-sop.md
@@ -76,18 +76,16 @@ Once the run is completed, a number of files will be available and you can doubl
 
 This includes a suggested_mask.csv file generated by the run with potentially problematic sites. If you start a new run with the same inputs and additionally provide this mask file in the menu, it will improve the alignment and phylogeny.
 
+---
 
 #### Related documents:
 This document is part of the MPXV sequencing protocol package:
-: [http://artic.network/mpxv/](http://artic.network/mpxv/)
-
-Setting up the laptop computing environment using Conda:
-: [http://artic.network/ebov/ebov-it-setup.html](http://artic.network/ebov/ebov-it-setup.html)
-
+: [http://artic.network/mpxv](http://artic.network/mpxv)
 
 
 <br /><br /><br />
 
 {% include wellcome-trust.html %}
+<br />
 
 <div class="pagebreak"> </div>
diff --git a/_resources/mpxv/mpxv-sequencing-guide.md b/_resources/mpxv/mpxv-sequencing-guide.md
@@ -126,4 +126,15 @@ ARTIC MPXV bioinformatics SOP \- to follow
 
 Squirrel \- *[https://github.com/aineniamh/squirrel*](https://github.com/aineniamh/squirrel)
 
+ ---
+
+> This document is part of the MPXV sequencing protocol package:
+: [http://artic.network/mpxv](http://artic.network/mpxv)
+
+<br /><br /><br />
+
+{% include wellcome-trust.html %}
+<br />
+
+<div class="pagebreak"> </div>