Nextstrain repository for measles virus

This repository contains three workflows for the analysis of measles 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/measles.

Installation

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

After you've installed the Nextstrain CLI, you can set up measles with

nextstrain setup measles

Quickstart

Run the default phylogenetic workflow via:

nextstrain run measles phylogenetic measles-analysis nextstrain view measles-analysis

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.