phylogenetic

Phylogenetic

This workflow uses metadata and sequences to produce one or multiple Nextstrain datasets that can be visualized in Auspice.

Resulting tree is available here: https://nextstrain.org/nipah

Background

See e.g. Whitmer et. al, 2020

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.

With nextstrain run

If you haven't set up the nipah pathogen, then set it up with:

nextstrain setup nipah

Otherwise, make sure you have the latest set up with:

nextstrain update nipah

Run the phylogenetic workflow with:

nextstrain run nipah phylogenetic <analysis-directory>

Your <analysis-directory> will contain the workflow's intermediate files and the final output auspice/nipah_{build}.json files.

You can view the result with

nextstrain view <analysis-directory>

With nextstrain build

If you don't have a local copy of the nipah repository, use Git to download it

git clone https://github.com/nextstrain/nipah.git

Otherwise, update your local copy of the workflow with:

cd nipah
git pull --ff-only origin main

Run the phylogenetic workflow workflow with

cd phylogenetic
nextstrain build .

The phylogenetic directory will contain the workflow's intermediate files and the final output auspice/nipah_{build}.json files .

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

nextstrain view .

Data Requirements

The core phylogenetic workflow will use metadata values as-is, so please do any desired data formatting and curations as part of the ingest workflow.

1. The metadata must include an ID column that can be used as as exact match for the sequence ID present in the FASTA headers.
2. The date column in the metadata must be in ISO 8601 date format (i.e. YYYY-MM-DD).
3. Ambiguous dates should be masked with XX (e.g. 2023-01-XX).

Defaults

The defaults directory contains all of the default configurations for the phylogenetic workflow.

defaults/config.yaml contains all of the default configuration parameters used for the phylogenetic workflow. Use Snakemake's --configfile/--config options to override these default values.

Snakefile and rules

The rules directory contains separate Snakefiles (*.smk) as modules of the core phylogenetic workflow. The modules of the workflow are in separate files to keep the main phylogenetic Snakefile succinct and organized.

Modules are all included in the main Snakefile in the order that they are expected to run.

Update example data

Example data should be updated occasionally. To update, run:

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