Docs: Add page of examples of using Augur

docs/examples.rst

@@ -0,0 +1,79 @@
+=======================
+Examples of using Augur
+=======================
+
+We really enjoy hearing about people using Augur.  If you use Augur to do your
+work, we'd love to add it to this page!  Let us know about it by `opening an
+issue <https://github.com/nextstrain/augur/issues/new?title=Augur%20in%20the%20wild>`__
+or `submitting a PR <https://github.com/nextstrain/augur/pulls>`__.
+
+
+Nextstrain tutorials
+====================
+
+There are three tutorials for getting started with Nextstrain that use Augur
+for all or part of the bioinformatics and analysis:
+
+The `Zika tutorial
+<https://nextstrain.org/docs/getting-started/zika-tutorial>`__ is a good
+starting point if you have FASTA files and some metadata about your sequences.
+The `accompanying build repository
+<https://github.com/nextstrain/zika-tutorial>`__ is a simplified version of the
+full Zika build.
+
+The `Tuberculosis tutorial
+<https://nextstrain.org/docs/getting-started/tb-tutorial>`__ is a good
+starting point if you have VCF files and some metadata about your sequences.
+It uses the `full Tuberculosis build repository
+<https://github.com/nextstrain/tb>`__.
+
+The `MERS / BEAST tutorial
+<https://github.com/nextstrain/mers-beast-tutorial>`__ is a good starting
+point if you have a `BEAST <https://beast.community/>`__ tree and want to use
+it with Augur and Auspice.
+
+
+Nextstrain pathogens
+====================
+
+All pathogens on `Nextstrain <https://nextstrain.org>`__ currently use Augur to
+go from raw data to `Auspice <https://github.com/nextstrain/auspice>`__-ready
+results files by performing cleanup, subsampling, alignment, tree building, and
+ancestral state reconstruction.
+
+Each pathogen has its own build repository on `GitHub <https://github.com>`__
+which uses `Snakemake <http://snakemake.readthedocs.io>`__ to define and run
+the pipeline of Augur commands.
+
+=============================================================   =======================================================================================
+Pathogen                                                        GitHub repository
+=============================================================   =======================================================================================
+`Seasonal influenza <https://nextstrain.org/flu/seasonal>`__    `nextstrain/seasonal-flu <https://github.com/nextstrain/seasonal-flu>`__
+`West Nile Virus <https://nextstrain.org/WNV>`__                `nextstrain/WNV <https://github.com/nextstrain/WNV>`__
+`Lassa <https://nextstrain.org/lassa>`__                        `nextstrain/lassa <https://github.com/nextstrain/lassa>`__
+`Mumps <https://nextstrain.org/mumps>`__                        `nextstrain/mumps <https://github.com/nextstrain/mumps>`__
+`Zika <https://nextstrain.org/zika>`__                          `nextstrain/zika <https://github.com/nextstrain/zika>`__
+`Ebola <https://nextstrain.org/ebola>`__                        `nextstrain/ebola <https://github.com/nextstrain/ebola>`__
+`Dengue <https://nextstrain.org/dengue>`__                      `nextstrain/dengue <https://github.com/nextstrain/dengue>`__
+`Avian influenza <https://nextstrain.org/flu/avian>`__          `nextstrain/avian-flu <https://github.com/nextstrain/avian-flu>`__
+`Measles <https://nextstrain.org/measles>`__                    `nextstrain/measles <https://github.com/nextstrain/measles>`__
+`Enterovirus D68 <https://nextstrain.org/enterovirus/d68>`__    `neherlab/enterovirus_nextstrain <https://github.com/neherlab/enterovirus_nextstrain>`__
+`Tuberculosis <https://nextstrain.org/tb>`__                    `nextstrain/tb <https://github.com/nextstrain/tb>`__
+=============================================================   =======================================================================================
+
+You can download a copy of a build repository, inspect the Augur commands used,
+and try running it locally yourself.  This can be useful to reproduce the
+analysis or tweak it for your own needs and data.
+
+
+Nextstrain community
+====================
+
+There are also some community-produced analyses on Nextstrain which use Augur:
+
+=================================================================================================   ==========================================================================
+Name                                                                                                GitHub repository
+=================================================================================================   ==========================================================================
+`Ebola epidemic in North Kivu, DRC <https://nextstrain.org/community/inrb-drc/ebola-nord-kivu>`__   `inrb-drc/ebola-nord-kivu <https://github.com/inrb-drc/ebola-nord-kivu>`__
+`Wheat yellow rust <https://nextstrain.org/community/SaundersLab/PST>`__                            `SaundersLab/PST <https://github.com/SaundersLab/PST>`__
+=================================================================================================   ==========================================================================

docs/index.rst

@@ -16,4 +16,5 @@ Augur originated as part of `Nextstrain <https://nextstrain.org>`__, an open-sou
    installation
    cli
    api
+   examples
    authors