Update top-level README

README.md

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 # 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)