NeoPredPipe: High-Throughput Neoantigen Prediction and Recognition Potential Pipeline

Next generation sequencing has yielded an unparalleled means of quickly determining the molecular make-up of patient tumors. In conjunction with emerging, effective immunotherapeutics for a number of cancers, this rapid data generation requires a paired high-throughput means of predicting neoantigens that may stimulate immune response. Here we offer NeoPredPipe as a contiguous means of predicting putative neoantigens and their corresponding recognition potentials for both single and multi-region tumor samples. NeoPredPipe is able to quickly provide summary information for researchers, and clinicians alike, on neoantigen burdens while providing high-level insights into tumor heterogeneity given somatic mutation calls and, optionally, patient HLA haplotypes.