This repository contains three workflows for the analysis of mpox virus (MPXV) data:

• ingest/ - Download data from GenBank, clean and curate it and upload it to S3
• phylogenetic/ - Filter sequences, align, construct phylogeny and export for visualization
• nextclade/ - Make Nextclade datasets for nextstrain/nextclade_data

Each folder contains a README.md with more information. The results of running both workflows are publicly visible at nextstrain.org/mpox.

Follow the standard installation instructions for Nextstrain's suite of software tools.

Run the default phylogenetic workflow via:

cd phylogenetic/
nextstrain build .
nextstrain view .

• Running a pathogen workflow
• Contributor documentation