Sequencing-based neutralization assays to measure neutralizing antibody titers of infant sera collected prior and following first exposure either through vaccination or infection.
Details about the viruses included in the library are in data/viral_libraries/.
This project uses the same viral library described in Loes et al, 2024. Design of the library and plasmids for strains including this library are available at https://github.com/jbloomlab/flu_seqneut_DRIVE_2021-22_repeat_vax/
Metadata about all relevant sera for which titers were measured is in data/sera_metadata/sera_metadata.csv.
All titers collected for infant serum are available in results/aggregated_titers/titers_PulendranCohort.csv
See the HTML documentation rendered at https://jbloomlab.github.io/flu_seqneut_FirstExposures/ for interactive plots summarizing the results (at the bottom of the page), as well as notebooks showing all neutralization curves and details on per-plate and per-serum quality control.
Summary plots are generated through non-pipeline analyses by the notebook available in https://jbloomlab.github.io/flu_seqneut_FirstExposures/notebooks/summarize_titers.ipynb.
This repository contains an analysis of the data using the Bloom lab software seqneut-pipeline as a submodule. See that repository for instructions on how to use Github submodules, including seqneut-pipeline.
The configuration for the analysis is in config.yml and the analysis itself is run by snakemake using Snakefile.
Input data are in ./data/, and all results created by the pipeline are placed in ./results/.
To run the pipeline, build the seqneut-pipeline conda environment from the environment.yml in seqneut-pipeline.
Then run the pipeline using:
snakemake -j <n_jobs> --software-deployment-method conda