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Augur: A bioinformatics toolkit for phylogenetic analysis
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    *One held to foretell events by omens.*
    (`Merriam-Webster <https://www.merriam-webster.com/dictionary/augur>`__)

.. note::
   The documentation you are viewing is Augur's reference guide, which means it is information-oriented and targeted at users who just need info about how Augur works.
    
   * If you have a question about how to achieve a specific goal with Augur, check out our :doc:`Augur-focused How-to Guides section <docs.nextstrain.org:guides/bioinformatics/index>` in the main Nextstrain documentation.
   * If you want to learn the basics of how to use Augur from scratch, check out our :doc:`Zika tutorial <docs.nextstrain.org:tutorials/zika_tutorial>` in the main Nextstrain documentation.
   * If you want to understand how Augur fits together with Auspice to visualize results, check out our :doc:`Data Formats section <docs.nextstrain.org:reference/formats/data-formats>` in the main Nextstrain documentation.



Augur is a bioinformatics toolkit to track evolution from sequence and serological data.
It provides a collection of commands which are designed to be composable into larger processing pipelines.
Augur originated as part of `Nextstrain <https://nextstrain.org>`__, an open-source project to harness the scientific and public health potential of pathogen genome data.
All source code is available on `GitHub <https://github.com/nextstrain/augur>`__.

.. note:: We have just released version 6 of augur -- `check our upgrading guide <releases/migrating-v5-v6.html>`__


Augur is composed of a series of modules and different workflows will use different parts of the pipeline.
A selection of augur modules and different possible entry points are illustrated below.

.. image:: figures/augur_analysis_sketch.png

The canonical pipeline would ingest sequences and metadata such as dates and sampling locations, filter the data, align the sequences, infer a tree, and export the results in a format that can be visualized by auspice.

In some cases, you might start with a manually curated alignment and want to start the workflow at the tree building step.
Or you already have a tree inferred. In this case, you only need to feed you tree through the ``refine`` and ``export`` steps.
The ``refine`` step is necessary to ensure that cross-referencing between tree nodes and meta data works as expected.

The different augur modules can be strung together by workflow managers like snakemake and nextflow.
The nextstrain team uses `snakemake <https://snakemake.readthedocs.io/en/stable/>`__ to run and manage the different analysis that you see on `nextstrain.org <https://nextstrain.org>`__.

.. toctree::
   :maxdepth: 2
   :caption: Table of contents
   :name: mastertoc
   :titlesonly:

   installation/installation
   usage/usage
   releases/releases
   faq/faq
   examples/examples
   api/api
   authors/authors
