nextstrain.org/nipah

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

• ingest/ - Download data from GenBank, clean and curate it, and upload a pair of sequence and metadata files 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.

After you've installed the Nextstrain CLI, you can set up nipah with

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