From 59f808bfef5aa22d5ddc470a6e05a7c47303eda3 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Mon, 28 Mar 2022 15:51:04 -0700
Subject: [PATCH] Create tutorial intro page using content from index pages
---
docs/src/index.rst | 10 +++-------
docs/src/tutorial/index.rst | 3 +--
docs/src/tutorial/intro.rst | 17 +++++++++++++++++
3 files changed, 21 insertions(+), 9 deletions(-)
create mode 100644 docs/src/tutorial/intro.rst
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.