Nextstrain repository for Oropouche virus

This repository contains two workflows for the analysis of Oropouche 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.

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 History 55 Commits
.github/workflows		.github/workflows
docs/nextstrain-internal		docs/nextstrain-internal
ingest		ingest
nextclade		nextclade
phylogenetic		phylogenetic
shared		shared
.gitattributes		.gitattributes
.gitignore		.gitignore
.pre-commit-config.yaml		.pre-commit-config.yaml
CHANGELOG.md		CHANGELOG.md
README.md		README.md
nextstrain-pathogen.yaml		nextstrain-pathogen.yaml