nextstrain.org/lassa

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

ingest/ - Download data from GenBank, clean and curate it, separate into L and S segments, 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 .