https://github.com/nextstrain/zika

Nextstrain build for Zika virus
https://github.com/nextstrain/zika

nextstrain pathogen

Last synced: 10 months ago
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Nextstrain build for Zika virus

• Host: GitHub
• URL: https://github.com/nextstrain/zika
• Owner: nextstrain
• Created: 2018-06-28T17:21:54.000Z (almost 8 years ago)
• Default Branch: main
• Last Pushed: 2024-12-16T23:09:02.000Z (over 1 year ago)
• Last Synced: 2024-12-17T00:27:02.041Z (over 1 year ago)
• Topics: nextstrain, pathogen
• Language: Python
• Homepage: https://nextstrain.org/zika
• Size: 370 KB
• Stars: 8
• Watchers: 18
• Forks: 11
• Open Issues: 6
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Contributing: CONTRIBUTING.md

Awesome Lists containing this project

README

          
# Nextstrain repository for Zika virus

This repository contains two workflows for the analysis of Zika 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/zika](https://nextstrain.org/zika).

## 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 zika with

    nextstrain setup zika

## Quickstart

Run the default phylogenetic workflow via:

    nextstrain run zika phylogenetic zika-analysis

    nextstrain view zika-analysis

## Documentation

- [Running a pathogen workflow](https://docs.nextstrain.org/en/latest/tutorials/running-a-workflow.html)

- [Contributor documentation](./CONTRIBUTING.md)