Phylogenetic Inference and Characterization of am4N1 Nueraminidases from North American A(H5N1) HPAI
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Matthew J. Wersebe, PhD
US Department of Health and Human Services (HHS)
Centers for Disease Control and Prevenetion (CDC)
National Center for Immunizations and Respiratory Diseases (NCIRD)
Influenza Division (ID)
Virology, Surveillance, and Diagnosis Branch (VSDB)
Public Release of phylogenetic inference code to related to the publication:
Authored by Wersebe 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 containers with dependencies are published to Dockerhub.
Example Installation:
$ git clone git@github.com:cdcent/am4N1Phylogenetics.git # Or use HTTPS/ GitHub CLI
$ cd am4N1Phylogenetics
$ 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 analysis.
-
am4N1_phylodynamics_config.yamlandam4N1_phylodynamics_workflow.smk: Produce a complete phylodynamic analysis of am4N1-like NA genes. -
global_phylogenetics_config.yamlandglobal_phylogenetics_workflow.smk: Produce a phylogenetic analysis of all observed NA-N1 genes.
These auspice JSON files can be uploaded visualized interactively on auspice.
In part, we analyzed data from GISAID and thus this data is subject to GISAID's Data Use Agreement and cannot be redistributed here.
Data analyzed from GISAID can be retrived using the EPI_SET index EPI_SET_251204qo and index EPI_SET_260209yr.
Otherwise, data downloaded and assembled from the NCBI Sequence Read Archive and coalesced with metadata from the NCBI Genbank database is indexed here with a persisent DOI. Additionally, you may find persistently indexed Auspice outputs here.
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