phylogenetic

nextstrain.org/mpox

This is the Nextstrain build for MPXV (mpox virus). Output from this build is visible at nextstrain.org/mpox. The lineages within the recent mpox outbreaks in humans are defined in a separate lineage-designation repository.

Software requirements

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

Usage

If you're unfamiliar with Nextstrain builds, you may want to follow our Running a Pathogen Workflow guide first and then come back here.

The easiest way to run this pathogen build is using the Nextstrain command-line tool from within the phylogenetic/ directory:

cd phylogenetic/
nextstrain build .

Once you've run the build, you can view the results with:

nextstrain view .

Example build

You can run an example build using the example data provided in this repository via:

nextstrain build .  --configfile build-configs/ci/config.yaml

When the build has finished running, view the output Auspice trees via:

nextstrain view .

Provision input data

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

• sequences.fasta.xz
• metadata.tsv.gz

The above datasets have been preprocessed and cleaned from GenBank using the ingest/ workflow and are updated at regular intervals.

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 . data/sequences.fasta.xz data/metadata.tsv.gz

Run analysis pipeline

Run pipeline to produce the "overview" tree for /mpox/all-clades with:

nextstrain build . --configfile defaults/mpxv/config.yaml

Run pipeline to produce the "clade IIb" tree for /mpox/clade-IIb with:

nextstrain build . --configfile defaults/hmpxv1/config.yaml

Run pipeline to produce the "lineage B.1" tree for /mpox/lineage-B.1 with:

nextstrain build . --configfile defaults/hmpxv1_big/config.yaml

Run pipeline to produce the "clade I" tree for /mpox/clade-I with:

nextstrain build . --configfile defaults/clade-i/config.yaml

Visualize results

View results with:

nextstrain view .

Configuration

The default configuration takes place in defaults/*/config.yaml files for each build. The analysis pipeline is contained in rules/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.

Custom build configs

The build-configs directory contains configs and customizations that override and/or extend the default workflow.

• chores - internal Nextstrain chores such as updating the example data.
• ci - CI build that run the example build with the example data.
• nextstrain-automation - internal Nextstrain automated builds

Update example data

Example data is used by CI. It can also be used as a small subset of real-world data.

Example data should be updated every time metadata schema is changed or a new clade/lineage emerges. To update, run:

nextstrain build . update_example_data -F \
    --configfiles build-configs/ci/config.yaml build-configs/chores/config.yaml

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.