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/ - Workflow which produces JSONs for visualisation in Auspice
• 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.

Documentation

• Running a pathogen workflow