From 658e40945f9b7b711712bdb3039ccca721e3925a Mon Sep 17 00:00:00 2001
From: Jover Lee <joverlee521@gmail.com>
Date: Fri, 19 Jan 2024 14:15:06 -0800
Subject: [PATCH 1/2] Add Quickstart section to the top level README

Mirroring changes made in https://github.com/nextstrain/zika/pull/30.
---
 README.md | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/README.md b/README.md
index 1b0e8d8..f2914be 100644
--- a/README.md
+++ b/README.md
@@ -10,6 +10,17 @@ This repository contains three workflows for the analysis of mpox virus (MPXV) d
 
 Each folder contains a README.md with more information.
 
+## Quickstart
+
+Follow the [standard installation instructions](https://docs.nextstrain.org/page/install.html) for Nextstrain's suite of software tools.
+
+Then run the default phylogenetic workflow via:
+```
+cd phylogenetic/
+nextstrain build .
+nextstrain view .
+```
+
 ## Documentation
 
 - [Contributor documentation](./CONTRIBUTING.md)

From c0811c56e91ca34b4ee91baeade109dfa98348cc Mon Sep 17 00:00:00 2001
From: Jover Lee <joverlee521@gmail.com>
Date: Fri, 19 Jan 2024 16:08:44 -0800
Subject: [PATCH 2/2] Further updates to READMEs

Copying over similar edits made in
https://github.com/nextstrain/zika/commit/85dd505b7eb1038def962541ad29ebe4b101519c

1. Installation section in top-level readme (I'm always looking for this)
2. Make it clearer that phylogenetic workflow needs to be run from within the phylogenetic/ directory

Co-authored-by: Trevor Bedford <trevor@bedford.io>
---
 README.md              | 13 ++++++++-----
 phylogenetic/README.md | 19 ++++++++++++++++++-
 2 files changed, 26 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index f2914be..af6da54 100644
--- a/README.md
+++ b/README.md
@@ -5,16 +5,18 @@
 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).
 
-## Quickstart
+## Installation
+
+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/page/install.html) for Nextstrain's suite of software tools.
+## Quickstart
 
-Then run the default phylogenetic workflow via:
+Run the default phylogenetic workflow via:
 ```
 cd phylogenetic/
 nextstrain build .
@@ -23,4 +25,5 @@ nextstrain view .
 
 ## Documentation
 
+- [Running a pathogen workflow](https://docs.nextstrain.org/en/latest/tutorials/running-a-workflow.html)
 - [Contributor documentation](./CONTRIBUTING.md)
diff --git a/phylogenetic/README.md b/phylogenetic/README.md
index 4e5c2d8..99c5d7c 100644
--- a/phylogenetic/README.md
+++ b/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.