Web app for visualizing pathogen evolution

Introduction

The nextstrain project is an attempt to make flexible informatic pipelines and visualization tools to track ongoing pathogen evolution as sequence data emerges. The nextstrain project derives from nextflu, which was specific to influenza evolution.

nextstrain is comprised of three components:

  • fauna: database and IO scripts for sequence and serological data
  • augur: informatic pipelines to conduct inferences from raw data
  • auspice: web app to visualize resulting inferences

Development

The current auspice repo is still very much a work-in-progress. We recommend that you use nextflu instead for current applications. At some point, this repo will takeover from the nextflu repo.

Auspice

Definition: Observation by an augur, ie a prophetic sign.

Auspice is the web app that gives an interactive display of inferences produced by augur pipeline.

Getting started

$ git clone ... $ cd ... $ npm install $ npm start

License and copyright

Copyright 2014-2016 Trevor Bedford, Richard Neher and Colin Megill.

Source code to nextstrain is made available under the terms of the GNU Affero General Public License (AGPL). nextstrain is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.