https://github.com/nextstrain/lassa
Nextstrain build for Lassa virus
https://github.com/nextstrain/lassa
nextstrain pathogen
Last synced: 10 months ago
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Nextstrain build for Lassa virus
- Host: GitHub
- URL: https://github.com/nextstrain/lassa
- Owner: nextstrain
- Created: 2018-07-20T05:39:42.000Z (almost 8 years ago)
- Default Branch: main
- Last Pushed: 2024-11-28T16:41:27.000Z (over 1 year ago)
- Last Synced: 2024-11-28T17:23:59.585Z (over 1 year ago)
- Topics: nextstrain, pathogen
- Language: Python
- Homepage: https://nextstrain.org/staging/lassa
- Size: 303 KB
- Stars: 0
- Watchers: 18
- Forks: 5
- Open Issues: 9
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Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# nextstrain.org/lassa
This repository contains two workflows for the analysis of Lassa virus data:
- [`ingest/`](./ingest) - Download data from GenBank, clean and curate it, separate into L and S segments, 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.
## 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)