A collection of resources and documents for the genome sequencing of Mpox virus (MPXV) using a tiled amplicon approach.
Resources and documents
Background
Mpox virus sequencing
A guide to sequencing for genomic epidemiology
Primer Scheme
artic-inrb-mpox/2500/v1.0.0 Primer Scheme
The ARTIC-network primer scheme for sequencing MPXV
Setup guides
EPI2ME Installation
A guide to help you install and set up EPI2ME from the EPI2ME team
User-interface pipelines using Epi2me
MPXV alignment and phylogenetics pipeline using Epi2Me
Squirrel | bioinformatics
amplicon-nf: Running the pipeline in EPI2ME for Illumina Data
Using EPI2ME for running the ARTIC amplicon-nf pipeline without the commandline
amplicon-nf: Running the pipeline in EPI2ME for Oxford Nanopore Data
Using EPI2ME for running the ARTIC amplicon-nf pipeline without the commandline
Command line interface pipeline SOPs
Fieldbioinformatics: viral amplicon sequencing bioinformatics SOP
Nanopore | bioinformatics