Merge pull request #229 from nextstrain/top-level-readme

Add Quickstart section to the top level README

README.md

@@ -5,11 +5,25 @@
 This repository contains three workflows for the analysis of mpox virus (MPXV) data:
 
 - [`ingest/`](./ingest) - Download data from GenBank, clean and curate it and upload it to S3
-- [`phylogenetic/`](./phylogenetic) - Make phylogenetic trees for nextstrain.org
+- [`phylogenetic/`](./phylogenetic) - Filter sequences, align, construct phylogeny and export for visualization
 - [`nextclade/`](./nextclade) - Make Nextclade datasets for nextstrain/nextclade_data
 
-Each folder contains a README.md with more information.
+Each folder contains a README.md with more information. The results of running both workflows are publicly visible at [nextstrain.org/mpox](https://nextstrain.org/mpox).
+
+## Installation
+
+Follow the [standard installation instructions](https://docs.nextstrain.org/en/latest/install.html) for Nextstrain's suite of software tools.
+
+## Quickstart
+
+Run the default phylogenetic workflow via:
+```
+cd phylogenetic/
+nextstrain build .
+nextstrain view .
+```
 
 ## Documentation
 
+- [Running a pathogen workflow](https://docs.nextstrain.org/en/latest/tutorials/running-a-workflow.html)
 - [Contributor documentation](./CONTRIBUTING.md)

phylogenetic/README.md

@@ -5,10 +5,24 @@ The lineages within the recent mpox outbreaks in humans are defined in a separat
 
 ## Software requirements
 
-Follow the [standard installation instructions](https://docs.nextstrain.org/en/latest/install.html) for Nextstrain's suite of software tools.
+Follow the [standard installation instructions](https://docs.nextstrain.org/en/latest/install.html)
+for Nextstrain's suite of software tools.
 
 ## Usage
 
+If you're unfamiliar with Nextstrain builds, you may want to follow our
+[Running a Pathogen Workflow guide][] first and then come back here.
+
+The easiest way to run this pathogen build is using the Nextstrain
+command-line tool from within the `phylogenetic/` directory:
+
+    cd phylogenetic/
+    nextstrain build .
+
+Once you've run the build, you can view the results with:
+
+    nextstrain view .
+
 ### Example build
 
 You can run an example build using the example data provided in this repository via:
@@ -30,6 +44,9 @@ Input sequences and metadata can be retrieved from data.nextstrain.org
 * [sequences.fasta.xz](https://data.nextstrain.org/files/workflows/mpox/sequences.fasta.xz)
 * [metadata.tsv.gz](https://data.nextstrain.org/files/workflows/mpox/metadata.tsv.gz)
 
+The above datasets have been preprocessed and cleaned from GenBank using the
+[ingest/](../ingest/) workflow and are updated at regular intervals.
+
 Note that these data are generously shared by many labs around the world.
 If you analyze and plan to publish using these data, please contact these labs first.