nextNEOpi: a comprehensive pipeline for computational neoantigen prediction.

Summary Somatic mutations and gene fusions can produce immunogenic neoantigens mediating anticancer immune responses. However, their computational prediction from sequencing data requires complex computational workflows to identify tumor-specific aberrations, derive the resulting peptides, infer patients' Human Leukocyte Antigen (HLA) types, and predict neoepitopes binding to them, together with a set of features underlying their immunogenicity. Here, we present nextNEOpi, a comprehensive and fully-automated bioinformatic pipeline to predict tumor neoantigens from raw DNA and RNA sequencing data. In addition, nextNEOpi quantifies neoepitope- and patient-specific features associated with tumor immunogenicity and response to immunotherapy. Availability and implementation nextNEOpi source code and documentation are available at https://github.com/icbi-lab/nextNEOpi. Supplementary information Supplementary data are available at Bioinformatics online.