https://github.com/nextstrain/rabies
https://github.com/nextstrain/rabies
nextstrain pathogen
Last synced: 7 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/nextstrain/rabies
- Owner: nextstrain
- Created: 2024-06-10T23:09:15.000Z (almost 2 years ago)
- Default Branch: main
- Last Pushed: 2025-01-17T19:58:43.000Z (over 1 year ago)
- Last Synced: 2025-02-11T13:29:07.615Z (over 1 year ago)
- Topics: nextstrain, pathogen
- Language: Python
- Homepage: https://nextstrain.org/rabies
- Size: 151 KB
- Stars: 0
- Watchers: 8
- Forks: 0
- Open Issues: 5
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Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
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README
# Nextstrain repository for rabies virus
This repository contains two workflows for the analysis of rabies virus data:
- [`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)