Sequencing-based neutralization to analyze titers of human serum samples from the DRIVE cohort against H1N1 virus after vaccination of individuals with one or two prior vaccinations.
Study by Loes et al (2024).
The final titers for each serum-virus pair are in results/aggregated_titers/titers_DRIVE.csv. The ./results/ also contains additional more detailed files with the per-viral-barcode counts for each sample, the fraction infectivities used to fit the neutralization curves, and details on the curve fits and titers for each individual replicate.
HTML documentation of analysis steps is rendered via GitHub Pages at https://jbloomlab.github.io/flu_seqneut_DRIVE_2021-22_repeat_vax/
This repository contains an analysis of the data using seqneut-pipeline.
Briefly, that pipeline is a submodule of this analysis.
The configuration for the analysis is in config.yml, the input data are in ./data/, the analysis itself is run by snakemake using Snakefile, the results are placed in ./results/, and HTML rendering of results is in ./docs/.
See seqneut-pipeline for more description of how the pipeline works.
In addition to running the pipeline itself, Snakefile also contains a few extra rules that run the Jupyter notebooks in ./notebooks/ to create some additional plots.
To run the pipeline, build the seqneut-pipeline conda environment in seqneut-pipeline/environment.yml.
Then run the pipeline using:
snakemake -j <n_jobs> --software-deployment-method conda
To run on the Hutch cluster, you can use the Bash scripts run_Hutch_cluster.bash.