https://github.com/nextstrain/mpox

Nextstrain build for mpox virus
https://github.com/nextstrain/mpox

augur auspice bioinformatics genbank genomic-epidemiology metadata monkeypox mpox nextstrain pathogen phylogenetics pipeline virus-evolution

Last synced: 21 days ago
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Nextstrain build for mpox virus

• Host: GitHub
• URL: https://github.com/nextstrain/mpox
• Owner: nextstrain
• License: mit
• Created: 2022-05-19T01:19:17.000Z (about 3 years ago)
• Default Branch: master
• Last Pushed: 2025-05-01T20:57:57.000Z (28 days ago)
• Last Synced: 2025-05-09T00:07:14.763Z (21 days ago)
• Topics: augur, auspice, bioinformatics, genbank, genomic-epidemiology, metadata, monkeypox, mpox, nextstrain, pathogen, phylogenetics, pipeline, virus-evolution
• Language: Python
• Homepage: https://nextstrain.org/mpox
• Size: 33.3 MB
• Stars: 46
• Watchers: 17
• Forks: 21
• Open Issues: 32
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE

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README

        
# Nextstrain repository for mpox virus

[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/nextstrain/mpox/master.svg)](https://results.pre-commit.ci/latest/github/nextstrain/mpox/master)

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

- [`ingest/`](./ingest) - Download data from GenBank, clean and curate it and upload it to S3

- [`phylogenetic/`](./phylogenetic) - Filter sequences, align, construct phylogeny and export for visualization

- [`nextclade/`](./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](https://nextstrain.org/mpox).

## Installation

Follow the [standard installation instructions](https://docs.nextstrain.org/en/latest/install.html) for Nextstrain's suite of software tools.

## Quickstart

Run the default phylogenetic workflow via:

```

cd phylogenetic/

nextstrain build .

nextstrain view .

```

## Documentation

- [Running a pathogen workflow](https://docs.nextstrain.org/en/latest/tutorials/running-a-workflow.html)

- [Contributor documentation](./CONTRIBUTING.md)