NextNEOpi: a comprehensive pipeline for computational neoantigen prediction.

ABSTRACT:

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.

SUBMITTER: Rieder D 

PROVIDER: S-EPMC8796378 | biostudies-literature |

REPOSITORIES: biostudies-literature