VDJtrack pipeline

An approach to evaluation of clonotype sampling in immune repertoire profiling time courses.

Contents:

• data/ the folder can be populated with data used in present study by running fetch_data.sh
• code/ all code used in this study
• example.Rmd and example/ a small example illustrating application of VDJtrack to monitor Yellow Fever Virus-specific clonotype induction at 2nd week post vaccination in a group of 6 volunteers

For comparing samples from different donor cohorts see the code/DLI_compare.Rmd template. Alternativey one can use example.Rmd with pooled samples by specifying CDR3s from samples of interest in the annotations.txt.