nextstrain.org/monkeypox

This is the Nextstrain build for monkeypox virus. Output from this build is visible at nextstrain.org/monkeypox.

Usage

Provision input data

Input sequences and metadata can be retrieved from data.nextstrain.org

Note that these data are generously shared by many labs around the world. If you analyze and plan to publish using these data, please contact these labs first.

Within the analysis pipeline, these data are fetched from data.nextstrain.org and written to data/ with:

nextstrain build --docker . data/sequences.fasta data/metadata.tsv

Run analysis pipeline

Run pipeline to produce "overview" tree for /monkeypox/mpxv with:

nextstrain build --docker --cpus 1 . --configfile config/config_mpxv.yaml

Run pipeline to produce "outbreak" tree for /monkeypox/hmpxv1 with:

nextstrain build --docker --cpus 1 . --configfile config/config_hmpxv1.yaml

Adjust the number of CPUs to what your machine has available you want to perform alignment and tree building a bit faster.

Visualize results

View results with:

nextstrain view auspice/

Configuration

Configuration takes place in config/config.yml by default. The analysis pipeline is contained in workflow/snakemake_rule/core.smk. This can be read top-to-bottom, each rule specifies its file inputs and output and pulls its parameters from config. There is little redirection and each rule should be able to be reasoned with on its own.

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.

Installation

Follow the standard installation instructions for Nextstrain's suite of software tools. Please choose the installation method for your operating system which uses Docker, as currently the pre-release version 2 of Nextalign and Nextclade is required which we've baked into nexstrain/base docker image.

Nextstrain build vs Snakemake

The above commands use the Nextstrain CLI and nextstrain build along with Docker to run using Nextalign v2. Alternatively, if you install Nextalign/Nextclade v2 locally you can run the pipeline with:

snakemake -j 1 -p --configfile config/config_mpxv.yaml
snakemake -j 1 -p --configfile config/config_hmpxv1.yaml

But you need to call the executable nextalign2 and nextclade2 respectively - since that's what they are called in the docker image.

Update colors to include new countries

Update colors_hmpxv1.tsv to group countries by region based on countries present in its metadata.tsv:

python3 scripts/update_colours.py --colors config/colors_hmpxv1.tsv \
    --metadata results/hmpxv1/metadata.tsv --output config/colors_hmpxv1.tsv

and similarly update colors_mpxv.tsv:

python3 scripts/update_colours.py --colors config/colors_mpxv.tsv \
    --metadata results/mpxv/metadata.tsv --output config/colors_mpxv.tsv

babarlelephant / monkeypox