Nextstrain repository for West Nile virus

This repository contains three workflows for the analysis of West Nile virus data:

• ingest/ - Download data from GenBank, clean and curate it
• phylogenetic/ - Filter sequences, align, construct phylogeny and export for visualization
• nextclade/ - Create nextclade datasets

Each folder contains a README.md with more information. The results of running both workflows are publicly visible at nextstrain.org/WNV.

Installation

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

Quickstart

Run the default phylogenetic workflow via:

cd phylogenetic/
nextstrain build .
nextstrain view .

Documentation

• Running a pathogen workflow

Working on this repo

This repo is configured to use pre-commit, to help automatically catch common coding errors and syntax issues with changes before they are committed to the repo. . If you will be writing new code or otherwise working within this repo, please do the following to get started:

1. install pre-commit by running either python -m pip install pre-commit or brew install pre-commit, depending on your preferred package management solution
2. install the local git hooks by running pre-commit install from the root of the repo
3. when problems are detected, correct them in your local working tree before committing them.

Note that these pre-commit checks are also run in a GitHub Action when changes are pushed to GitHub, so correcting issues locally will prevent extra cycles of correction.