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This repository holds the build code for generating a nextstrain tree with escape score predictions.

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matsengrp/LASV-manuscript-nextstrain-dmsa

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LASV manuscript repo for nextstrain w/ dmsa_pred

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 GPC sequences and metadata

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

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).

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This repository holds the build code for generating a nextstrain tree with escape score predictions.

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