https://github.com/nextstrain/nipah
https://github.com/nextstrain/nipah
nextstrain pathogen
Last synced: about 1 month ago
JSON representation
- Host: GitHub
- URL: https://github.com/nextstrain/nipah
- Owner: nextstrain
- Created: 2023-09-17T15:01:15.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2026-06-09T16:25:53.000Z (about 1 month ago)
- Last Synced: 2026-06-09T18:13:45.133Z (about 1 month ago)
- Topics: nextstrain, pathogen
- Language: Python
- Homepage: https://nextstrain.org/nipah
- Size: 312 KB
- Stars: 2
- Watchers: 6
- Forks: 0
- Open Issues: 2
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Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
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README
# nextstrain.org/nipah
This repository contains two workflows for the analysis of Nipah virus data:
- [`ingest/`](./ingest) - Download data from GenBank, clean and curate it, and upload a pair of sequence and metadata files to S3
- [`phylogenetic/`](./phylogenetic) - Filter sequences, align, construct phylogeny and export for visualization.
Each folder contains a README.md with more information.
## Installation
Follow the [standard installation instructions](https://docs.nextstrain.org/en/latest/install.html) for Nextstrain's suite of software tools.
After you've installed the Nextstrain CLI, you can set up nipah with
```bash
nextstrain setup nipah
```
## Quickstart
Run the default phylogenetic workflow via:
```
mkdir nipah-analysis
nextstrain run nipah phylogenetic nipah-analysis
nextstrain view nipah-analysis
```
## Documentation
- [Running a pathogen workflow](https://docs.nextstrain.org/en/latest/tutorials/running-a-workflow.html)