diff --git a/docs/src/index.rst b/docs/src/index.rst index 9e935bdd4..2e44f1bc3 100644 --- a/docs/src/index.rst +++ b/docs/src/index.rst @@ -2,15 +2,11 @@ A Getting Started Guide to the Genomic Epidemiology of SARS-CoV-2 ***************************************************************** -This template and tutorial will walk you through the process of running a basic phylogenetic analysis on SARS-CoV-2 data. -We've created these resources with the goal of enabling Departments of Public Health to start using Nextstrain to understand their SARS-CoV-2 genomic data within 1-2 hours. -In addition to the phylogenetic analysis described here, you can use our "drag-and-drop" tool for a clade assignment, mutations calling, and basic sequence quality checks at `clades.nextstrain.org `_. - -If you prefer video format to working through this tutorial in the written documentation, check out the :doc:`video tutorial walkthrough `. +This is the documentation for the SARS-CoV-2 workflow maintained and actively used by the Nextstrain core team. -We also recommend `this 1-hour video overview `_ by Heather Blankenship on how to deploy Nextstrain for a Public Health lab. +In addition to the phylogenetic analysis described here, you can use our "drag-and-drop" tool for a clade assignment, mutations calling, and basic sequence quality checks at `clades.nextstrain.org `_. -If something in this tutorial is broken or unclear, please `open an issue `_ so we can improve it for everyone. +If something in this documentation is broken or unclear, please `open an issue `_ so we can improve it for everyone. If you have a specific question, post a note over at the `discussion board `_ -- we're happy to help! diff --git a/docs/src/tutorial/index.rst b/docs/src/tutorial/index.rst index 670fcb05d..b5a89a97b 100644 --- a/docs/src/tutorial/index.rst +++ b/docs/src/tutorial/index.rst @@ -2,12 +2,11 @@ Tutorial ******** -These tutorials will guide you to create a :term:`Nextstrain build ` for genomic surveillance. - .. toctree:: :maxdepth: 1 :titlesonly: :caption: Table of contents + intro setup running diff --git a/docs/src/tutorial/intro.rst b/docs/src/tutorial/intro.rst new file mode 100644 index 000000000..b81ce9915 --- /dev/null +++ b/docs/src/tutorial/intro.rst @@ -0,0 +1,17 @@ +Introduction +============ + +These tutorials will walk you through the process of running a basic genomic surveillance workflow using SARS-CoV-2 data. +We've created these resources with the goal of enabling Departments of Public Health to start using Nextstrain to understand their SARS-CoV-2 genomic data within 1-2 hours. + +At the end, you will be able to: + +- create phylogenetic trees of SARS-CoV-2 genomes from different sources including GISAID and Nextstrain-curated GenBank data +- visualize the resulting trees in :term:`docs.nextstrain.org:Auspice` +- define subsampling logic for your own genomic epidemiological analysis + +After completing these tutorials, you may wish to `learn more about genomic epidemiology `_ or `review all possible options to configure your SARS-CoV-2 analyses with Nextstrain <../reference/configuration.html>`_. + +If you prefer video format to working through these written tutorials, check out the :doc:`video tutorial walkthrough <../videos>`. + +We also recommend `this 1-hour video overview `_ by Heather Blankenship on how to deploy Nextstrain for a Public Health lab.