Pipeline components for real-time virus analysis

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

Augur

Definition: One held to foretell events by omens.

Augur is the informatic processing pipeline to track evolution from sequence and serological data. It is broken into two parts, termed prepare and process, which result in output JSONs for Auspice (click for documentation).

flowchart

How to run:

License and copyright

Copyright 2014-2016 Trevor Bedford and Richard Neher.

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.