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Nextstrain build for mpox virus

Home Page: https://nextstrain.org/mpox

License: MIT License

Python 86.94% Shell 12.66% Perl 0.40%
monkeypox phylogenetics augur auspice bioinformatics genbank genomic-epidemiology metadata nextstrain pipeline

mpox's Introduction

Nextstrain repository for mpox virus

pre-commit.ci status

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.

Installation

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

Quickstart

Run the default phylogenetic workflow via:

cd phylogenetic/
nextstrain build .
nextstrain view .

Documentation

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