A CUDA-based program for doing fast clone collapsing of B and T cell immune repertoires using DBSCAN.
This package is created using CMAKE. Within the main folder of this package, just type
cmake .
and then
make
Within the main folder, start the program with
./psdbscan
This will process the file "data/ExampleData.csv" using the configuration file "data/psdbscan.conf". The output file and a log will be found in folder "data".
If you need some help for program options, just type
./psdbscan --help
This program uses a typical output of IMGT or other systems containing information about V, D and J genes as well as CDR3 sequences to do a clone collapsing using the DBSCAN clustering algorithm.
The configuration file is written in the INFO file format described for the BOOST package "property_tree"- It's nearly self-explaining.