Minimap2 lr:hq preset testing
Evaluating minimap2’s lr:hq preset for bacterial nanopore variant calling Introduction Oxford Nanopore Technologies (ONT) sequencing accuracy has improved dramatically in recent years. With basecalling models like Dorado v5.2.0 super-accuracy (sup), error rates are consistently hovering around the 1% mark. To match this shift in raw read quality, minimap2[1] introduced the lr:hq preset in version 2.27 (March 2024), which is calibrated for long reads with an error rate of <1%. This introduction was driven by internal benchmarking from ONT developers (see minimap2 issue #1127) who found that -x map-ont -k19 -w19 -U50,500 maximised both speed and downstream accuracy for high-quality reads. As such, the lr:hq preset was added to mirror those options. ...