Sub-consensus haploid variant calling in long-read sequencing technology

Background

Next-generation sequencing (NGS) is vital for tracking viral evolution during outbreaks. Oxford Nanopore Technologies (ONT) offers long-read, cost-effective sequencing, but accurate sub-consensus variant detection remains challenging. LoFreq, a widely used caller for sub-consensus variant calling in haploid genomes, was designed for short reads. This study assesses and benchmarks LoFreq variant identification accuracy on long-read data and proposes a calibration method to improve accuracy.