Preprint benchmarks Nanopore R10.4.1 chemistry and basecalling models for forensic STR profiling

A preprint deposited on bioRxiv reports a systematic benchmark of Oxford Nanopore Technologies R10.4.1 flow cell chemistry combined with several basecalling model tiers — HAC (high accuracy), SUP (super accuracy), and HYP (hyperbolic) — across multiple software versions, for the purpose of forensic short tandem repeat (STR) profiling.

STR profiling, the determination of repeat-count alleles at a standard set of autosomal loci alongside Y-chromosome STR markers, is the foundation of forensic DNA identification. Capillary electrophoresis (CE) has been the standard method for decades. Nanopore sequencing offers potential advantages in portability, cost, and performance with degraded samples, but historically elevated per-base error rates have limited its adoption in forensic applications where allele-calling accuracy is paramount.

The authors evaluated concordance between Nanopore-derived STR calls and established CE profiles across a panel of samples, testing how basecalling model choice and software version affect allele-calling accuracy for both autosomal and Y-STR loci. Newer basecalling models and chemistry showed substantially improved performance, with HYP-tier basecalling on R10.4.1 achieving accuracy levels that the authors suggest may be approaching forensic suitability.

The study will be of particular interest to forensic geneticists, researchers in sequencing methods, and population geneticists who use STR data. It does not constitute a validated forensic workflow. The preprint has not yet been peer-reviewed.