Seasonal influenza analysis of antigenic evolution in ILI data for Perofsky et al. 2024 (https://doi.org/10.7554/eLife.91849.1).
Run the flu analyses locally with no more than 4 cores.
snakemake -j 4 --use-conda
Alternately, distribute the analysis on a cluster with a Snakemake profile. The following command runs all analyses on the Hutch SLURM cluster, using mamba as the conda frontend for faster installation of environment packages.
snakemake --profile profiles/slurm-drmaa/
View the trees locally.
auspice view --datasetDir auspice/
All five replicate trees for HA and NA live at https://nextstrain.org/groups/blab/ under the keyword "perofsky-ili-antigenicity". For example, the first replicate HA tree can be found at https://nextstrain.org/groups/blab/perofsky-ili-antigenicity/flu/seasonal/h3n2/ha/21y/north-america/0
Summary data per strain live in auspice_tables/ per region and gene segment.