nextclade

Nextclade reference tree workflow for monkeypox

This README doesn't end up in the datasets, so it's a developer README, rather than a dataset user README.

Usage

snakemake

You need to have a nextclade3 binary in your path. It's in the nextstrain/docker-base image or you can get it from https://github.com/nextstrain/nextclade/releases/tag/3.0.0-alpha.0.

Visualize results

View results with:

nextstrain view auspice/

Maintenance

Updating for new clades

• Update each config/{build}/clades.tsv with new clades
• Add new clades to color ordering
• Add representative sequences to resources/include_accessions.txt
• Check that clades look good, exclude problematic sequences as necessary

Creating a new dataset version

• Edit CHANGELOG.md
• Switch to nextclade_data/data/mpox repo
• Create branch there, copy datasets, commit, push, open PR:

cd ~/code
cp mpox/nextclade/datasets/all-clades/tree.json nextclade_data/data/nextstrain/mpox/all-clades/tree.json
cp mpox/nextclade/datasets/clade-iib/tree.json nextclade_data/data/nextstrain/mpox/clade_iib/tree.json
p mpox/nextclade/datasets/lineage-b.1/tree.json nextclade_data/data/nextstrain/mpox/lineage-b.1/tree.json

Configuration

Builds differ in paths, relevant configs are pulled in through lookup.

Installation

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

Data use

We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequences and metadata for sharing their work. Please note that although data generators have generously shared data in an open fashion, that does not mean there should be free license to publish on this data. Data generators should be cited where possible and collaborations should be sought in some circumstances. Please try to avoid scooping someone else's work. Reach out if uncertain.