NeoFuse

NeoFuse is a user-friendly pipeline for the prediction of fusion neoantigens from tumor RNA-seq data.

NeoFuse takes single-sample FASTQ files of RNA-seq reads (single- or paired-end) as input and predicts putative fusion neoantigens through five main analytical steps:

• Genotyping of class-I Human Leukocyte Antigen (HLA) genes at 4-digit resolution.
• Prediction of fusion peptides and corresponding confidence scores.
• Prediction of peptide-HLA binding affinity as IC50 and percentile rank.
• Quantification of gene expression levels.
• Selection and annotation of putative fusion neoantigens based on binding affinity, confidence score, and gene expression.