This repository contains a nexstrain build for Lassa virus GPC with predicted antibody escape scores mapped onto the tree. The analysis is performed using the dmsa_pred package. This repo is currently set up to run the data as presented in the manuscript Deep mutational scanning reveals functional constraints and antigenic variability of Lassa virus glycoprotein complex.
For those unfamiliar with Nextstrain, we recommend checking out the Nextstrain documentation before reading further.
To run the pipeline, install snakemake following their documentation, This pipeline has been tested with versions >= 8.4.11
then clone this repository and the submodules
git clone https://github.com/matsengrp/LASV-manuscript-nextstrain-dmsa.git --recurse-submodules
Run the pipeline with the following command
snakemake --use-conda --cores 2 --configfile config/config.yaml
Alternatively, the pipeline can be run on a server via Slurm with the following command:
sbatch run_snakemake_cluster.bash
Each rule currently uses the environment specified in
my_profiles/dmsa_pred/dmsa_env.yaml.
The configuration file specified above provides paths to the
Lassa GPC sequences and escape data within the
LASV_Josiah_GP_DMS submodule.
The pipeline will output a JSON file(s) under the auspice/ directory
that can be visualized with auspice software.
CSV's of phenotype predictions can be found under results/dmsa-phenotype/
Lassa virus GPC sequences and metadata are downloaded as described in the LASV_phylogeny_analysis directory that is part of the LASV_Josiah_GP_DMS repository.
Configuration takes place within the Snakefile and the config/config.yaml files. The Snakefile can be read top-to-bottom, each rule
specifies its file inputs and output and also its parameters. The config/config.yaml is important for configuring the DMSA phenotype prediction component of this build (e.g., paths to the deep mutational scanning directories for escape data).