initial edits

_resources/mpxv/mpxv-it-setup.md

@@ -2,7 +2,7 @@
 title: "Mpox virus sequencing | IT setup guide"
 keywords: protocol
 layout: document
-last_updated: Jan 22, 2020
+last_updated: Aug 20 2024
 tags: [protocol] 
 permalink: # /mpxv/mpxv-it-setup.html
 folder: mpxv
@@ -21,18 +21,18 @@ category: # mpxv-setup
 
 {% include callout.html
 type='default'
-content='**Overview:** Instructions for setting up the laptop computing environment for running the MinION sequencer and performing the bioinformatics and downstream phylogenetic analyses.'
+content='**Overview:** Instructions for setting up a computing environment for running the MinION sequencer and performing the bioinformatics and downstream phylogenetic analyses.'
 %}
 
 <br />
 
-This document is part of the nCoV-2019 Nanopore sequencing protocol package:
-: [http://artic.network/ncov-2019](http://artic.network/ncov-2019)
+This document is part of the MPXV sequencing protocol package:
+: [http://artic.network/mpxv](http://artic.network/ncov-2019)
 
 #### Related documents:
 
-nCoV-2019 Nanopore bioinformatics protocol:
-: [http://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html](http://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html)
+MPXV nanopore bioinformatics protocol:
+: [http://artic.network/mpxv/mpxv-bioinformatics-sop.html](http://artic.network/mpxv/mpxv-bioinformatics-sop.html)
 
 <br /><br />
 
@@ -53,6 +53,14 @@ Laptop requirements for MinION:
 
 ## Software Setup
 
+https://labs.epi2me.io
+
+https://labs.epi2me.io/downloads/
+
+The current version of the EPI2ME Desktop application is v5.1.14
+
+https://www.docker.com/products/docker-desktop/
+
 These protocols instructions assume a 64-bit UNIX, Linux or similar environment. This could be Mac OS X (Yosemite or later), Linux (e.g., Ubuntu 16 or later), or Windows 10  Subsystem for Linux. It assumes familiarity with a UNIX-like *bash* command-line. 
 
 The steps in this document should be done and tested prior to sequencing, particularly if this will be done in an environment without internet access or where this is slow or unreliable. Once this is done, the bioinformatics and phylogenetics protocols can be performed largely off-line.