Phylogenetic inference for human H5N1 cases in the United States (2024-2025)
Matthew Wersebe
US Department of Health and Human Services (DHHS),
Centers for Disease Control and Prevention (CDC),
National Center for Immunizations and Respiratory Diseases (NCIRD),
Influenza Division (ID),
Virology Surveillance and Diagnostics Branch (VSDB)
Public Release of CDC's phylogenetic analysis of human A(H5N1) cases in the United States occurring in 2024 and 2025.
This work supports the publication: Next-generation sequencing strategies during the 2024-2025 avian influenza A(H5N1) Emergency Response in the U.S..
Authored by Frederick et al.
This workflow is primarily designed to work on a system running a Linux-based OS. However, scripts can be ported to run on MacOS or Windows as desired but these OS are not supported by default. The primary workflow is containerized using Docker and singularity which provides for additional reproducibility.
Basic Requirements:
Linux-OS with Mamba or Conda package manager and singularity.
Installation of Snakemake with the required software dependencies can be accomplished using the Mamba or Conda package manager. Dependencies are listed in the Snakemake_env.yaml yaml file stored within the Conda directory of this Repo. The remaining workflow dependencies rely on singularity containers and will be automatically handled by Snakemake if singularity is installed on your machine. Singularity can be installed by following the directions available here. The containers can be recreated using the Dockerfile specifications within the Docker directory in this repo. Otherwise the R and the Python dependencies are published to Dockerhub.
Example Installation:
$ git clone git@github.com:uee9/HumanH5N1Phylogenetics.git
$ cd HumanH5N1Phylogenetics
$ mamba env create -n Snakemake -f Conda/Snakemake_env.yaml
$ conda activate Snakemake
The underlying processes are written in R or make calls to augur or other command line programs and are ochestrated by snakemake. The workflow can be initiated from the command line. The required input data is provided in the Data directory. Additionally, you'll find GISAID acknowledgements for any data used from the epiflu platform.
Example usage:
$ snakemake --snakefile workflow.smk --configfile config.yaml --cores all --use-singularity --singularity-args "-H $(pwd)"
The workflow may take several hours to complete depending on the resources available on your machine.
The workflow will produce two auspice compatible JSON files for each pipeline and segment combination defined in the config.yaml.
The contents of output upon successful completion:
D1.1 Genotype Samples:
output/D11_HA.json
output/D11_HA_tip-frequencies.json
outout/D11_NA.json
output/D11_NA_tip-frequencies.json
output/D11_PB2.json
output/D11_PB2_tip-frequencies.json
B3.13 Genotype Samples:
output/B313_HA.json
output/B313_HA_tip-frequencies.json
output/B313_NA.json
output/B313_NA_tip-frequencies.json
output/B313_PB2.json
output/B313_PB2_tip-frequencies.json
These auspice JSON files can be uploaded visualized interactively on auspice.
The GISAID data analyzed here is available as a GISAID Epi_Set at the accession EPI_SET_260212nr.
For access to records indexed on NCBI/SRA and NCBI/Nucloetide please see the code base available at: NCBIH5N1MetadataParser.
This repository constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This repository is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the CC0 1.0 Universal public domain dedication. All contributions to this repository will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.
The repository utilizes code licensed under the terms of the Apache Software License and therefore is licensed under ASL v2 or later.
This source code in this repository is free: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version.
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Anyone is encouraged to contribute to the repository by forking and submitting a pull request. (If you are new to GitHub, you might start with a basic tutorial.) By contributing to this project, you grant a world-wide, royalty-free, perpetual, irrevocable, non-exclusive, transferable license to all users under the terms of the Apache Software License v2 or later.
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