Mpox virus (MPXV) resources

Background

Mpox virus sequencing | A guide to sequencing for genomic epidemiology

This is an overview guide and set of recommendations for MPXV genome sequencing with an emphasis on genomic epidemiology.

Setup Guides

Setting up and using EPI2ME for MPXV analysis pipelines

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.

MPXV sequencing

ARTIC/INRB Clade-independent Primer Schemes

2500 bp primer scheme Clade-I reference, Clade II reference, PCR amplification protocol for 2500 bp

400 bp primer scheme Clade-I reference, Clade II reference, PCR amplification protocol for 400 bp

Tiled amplicon sequencing protocol and primer scheme for MPXV

Chen et al. Yale amplicon sequencing protocol - dx.doi.org/10.17504/protocols.io.5qpvob1nbl4o/v4

This protocol is a primer scheme and validation for MPXV of the ARTIC SARS-CoV-2 tiled amplicon protocol

Bioinformatics pipeplines

Running the ARTIC nanopore bioinformatics pipeline using EPI2ME

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.

Running a bioinformatics pipeline for Illumina data using EPI2ME

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.

Running the ARTIC nanopore bioinformatics pipeline using the command line

This document provides detailed instructions for running the ARTIC fieldbioinformatics pipeline for MPXV on the command-line. This is useful to review what the pipeline does and how it works and for debugging issues for particular datasets.

Analysis pipeline

Running the Squirrel MPXV alignment and phylogenetics pipeline using EPI2ME

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.

Further Reading / Viewing

EPI2ME Labs - https://labs.epi2me.io/

ARTIC-CLIMB workshop videos (covering SARS-CoV-2 but generally applicable to MPXV) - https://www.climb.ac.uk/artic-and-climb-big-data-joint-workshop-2/

Chen et al. Yale amplicon sequencing protocol - https://www.protocols.io/view/monkeypox-virus-multiplexed-pcr-amplicon-sequencin-5qpvob1nbl4o

Squirrel - *https://github.com/aineniamh/squirrel*

Funded by the Wellcome Trust

Collaborators Award 206298/Z/17/Z --- ARTIC network