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.
Follow the standard installation instructions for Nextstrain's suite of software tools.
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 .
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 .
Input sequences and metadata can be retrieved from data.nextstrain.org
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 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
View results with:
nextstrain view .
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.
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
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
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.