BREAKFAST

Overview

BREAKFAST is a gene fusion detection tool for RNA-seq data that identifies chimeric transcripts using split-read and discordant-pair evidence. It was developed with a focus on detecting rearrangements in cancer genomes and was used as one of three complementary callers in the TCGA pan-cancer fusion landscape analysis.

Used by

• One of three RNA-seq fusion callers in the TCGA pan-cancer fusion analysis across 9,624 tumor samples spanning 33 cancer types; used alongside STAR-Fusion and EricScript with 5 kb and 100 kb minimum-distance cutoffs to reduce readthrough artifacts PMID:29617662

Notes

• Applied with minimum inter-gene distance cutoffs to reduce false-positive readthrough fusions.
• Multi-tool consensus (support from ≥2 callers) increases confidence in reported fusions.

Sources

This page was processed by entity-page-writer on 2026-05-15.