Nextstrain repository for Zika virus

This repository contains two workflows for the analysis of Zika virus data:

• ingest/ - Download data from GenBank, clean and curate it and upload it to S3
• phylogenetic/ - Filter sequences, align, construct phylogeny and export for visualization

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

Installation

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

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

nextstrain setup zika

Quickstart

Run the default phylogenetic workflow via:

nextstrain run zika phylogenetic zika-analysis
nextstrain view zika-analysis

Documentation

• Running a pathogen workflow
• Contributor documentation