About

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This repository analyzes West Nile Viral (WNV) genomes using Nextstrain to understand the circulation and transmission of WNV within the United States. This repository was developed based on the WNV repository used for the Twenty years of West Nile Virus in the Americas Nextstrain Narrative

Data

This build pulls WNV genomes that are publicly available from NCBI.

Installation

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

Clone this repository

git clone https://github.com/nextstrain/WNV.git
cd WNV

Try running Augur and Auspice

augur -help
auspice -help

Run the build

The build can be run at once or by workflows. Running the build by workflows can be helpful when troubleshooting or when testing modifications. To run the build by workflows first run the ingest workflow

nextstrain build ingest

Inside the ingest folder there should be two output files: metadata_all.tsv and sequences_all.tsv

Run the phylogenetic workflow

nextstrain build phylogenetic

Inside the phylogenetic folder there should be at least one output file: WNV-nextstrain_NA.json

Run the build all at once

nextstrain build

File Structure

This Nextstrain build follows the structure detailed in the [Pathogen Repo Guide] (https://github.com/nextstrain/pathogen-repo-guide)