From ecd309c6d4a6f71b3431dbf76d02533e93720642 Mon Sep 17 00:00:00 2001
From: Kim Andrews <17375001+kimandrews@users.noreply.github.com>
Date: Wed, 17 Jul 2024 16:37:18 -0700
Subject: [PATCH] Update top-level README

---
 README.md | 24 +++++++++++++++++++++++-
 1 file changed, 23 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 9747d20..d7a991a 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,25 @@
 # Nextstrain repository for rabies virus
+This repository contains two workflows for the analysis of rabies virus data:
 
-This repo is under development.
+- [`ingest/`](./ingest) - Download data from GenBank, clean and curate it and upload it to S3
+- [`phylogenetic/`](./phylogenetic) - Filter sequences, align, construct phylogeny and export for visualization
+
+Each folder contains a README.md with more information. The results of running both workflows are publicly visible at [nextstrain.org/rabies](https://nextstrain.org/rabies).
+
+## 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)