STRspy2.0: Unlocking the Potential of Long Reads for Forensic DNA Profiling

Abstract

Forensic human identification relies on length-based differences in short tandem repeats (STRs) across autosomal and Y chromosomes, which require separate reactions and provide limited resolution. While next-generation sequencing offers greater discriminatory power, most platforms are expensive and restricted to traditional lab settings. Nanopore sequencing has the potential to change this with the real-time, portable MinION sequencer. However, forensic-specific tools that generate STR profiles compatible with established length-based databases are lacking. To address this, we developed STRspy2.0, which simultaneously profiles autosomal and Y-STRs using nanopore reads. STRspy2.0 produced accurate profiles for 54 multiplexed control libraries and 41 mock casework samples (blood, swab, bone), achieving overall F1-scores of 100% and 99.75%, respectively. It maintains compatibility with existing forensic databases while providing higher resolution than traditional profiles. Our updated method and comprehensive database, along with the MinION’s small size and price, make sequence-based STR profiling more accessible to forensic laboratories and resource-limited settings.