Current corpus readout
- HiFi currently looks strongest for general-purpose variant-calling accuracy in this corpus.
- ONT looks strongest where native-DNA properties matter, especially methylation-aware workflows and flexible large-scale deployment.
Evidence in this corpus
- Mahmoud 2024 argues most clearly that HiFi gives the best overall small- and large-variant accuracy in its pilot comparisons.
- Hard 2023 uses PacBio HiFi for single-cell long-read work where per-read accuracy is critical.
- Showpnil 2024 uses HiFi for breakpoint-level rare disease resolution.
- Otsuki 2022, Sinha 2025, and Schloissnig 2025 show strong ONT use in population and clinical workflows.
Practical interpretation
- If the main target is maximal variant accuracy across small and large variants, HiFi currently has the cleaner case in this corpus.
- If the workflow needs native methylation, flexible deployment, or large-scale long-read acquisition, ONT has strong representation here.
Open questions
- How quickly does ONT duplex or later chemistry narrow the current HiFi accuracy edge?
- Which clinical use cases genuinely need HiFi, and which are already well served by ONT plus strong downstream filtering?