Nextstrain repository for Zika virus

This repository contains two workflows for the analysis of Zika virus data:

ingest/ - Download data from GenBank, clean and curate it and upload it to S3
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.

Installation

Follow the standard installation instructions for Nextstrain's suite of software tools.

Run the default phylogenetic workflow via:

cd phylogenetic/
nextstrain build .
nextstrain view .

Name	Name	Last commit message	Last commit date
Latest commit joverlee521 Merge pull request #79 from nextstrain/remove-ncov-ingest-geolocation… Mar 4, 2025 1daa5e0 · Mar 4, 2025 History 216 Commits
.github	.github	CI: Switch CI to `pathogen-repo-ci` workflow	Jul 16, 2024
ingest	ingest	ingest: Remove use of ncov-ingest geolocation rules	Feb 13, 2025
phylogenetic	phylogenetic	Update example data	Dec 16, 2024
.gitattributes	.gitattributes	Add .gitattributes file	Jul 17, 2024
.gitignore	.gitignore	Ignore snakemake state dir for current and subfolders	Dec 5, 2023
CHANGELOG.md	CHANGELOG.md	Add CHANGELOG (#39 )	Feb 27, 2024
CONTRIBUTING.md	CONTRIBUTING.md	Update Contributing docs	Jan 18, 2024
README.md	README.md	Further updates to READMEs	Jan 19, 2024
nextstrain-pathogen.yaml	nextstrain-pathogen.yaml	add nextstrain-pathogen.yaml [#60 ]	Jun 5, 2024