Markup | Genome Research

Table 2.

Performance metrics for long-read STR genotypers on the HG002 benchmark subset

Caller	Precision	Recall	Accuracy	F1	Avg. TruScore	% called
HG002, PacBio HiFi, ∼32× coverage
STRkit	0.9717	0.9545	0.9766	0.9631	98.85	99.88%
STRkit (-SNV)	0.9701	0.9487	0.9742	0.9593	98.62	99.87%
LongTR	0.9570	0.9541	0.9738	0.9555	98.80	99.63%
Straglr	N/A					97.18%
STRdust	0.7911	0.8790	0.8862	0.8327	95.72	99.84%
TRGT	0.9474	0.9675	0.9722	0.9574	98.80	99.87%
HG002, ONT R10 Simplex, ∼32× coverage
STRkit	0.9594	0.9494	0.9709	0.9544	98.44	99.90%
STRkit (-SNV)	0.9488	0.9394	0.9641	0.9440	98.14	99.88%
LongTR	0.9312	0.9397	0.9613	0.9354	98.24	99.70%
Straglr	N/A					96.86%
STRdust	0.6701	0.8727	0.8237	0.7581	94.80	99.63%
HG002, ONT R10 Duplex, ∼12× coverage
STRkit	0.9098	0.9004	0.9435	0.9051	96.03	99.78%
STRkit (-SNV)	0.8980	0.8924	0.9373	0.8952	95.66	99.76%
LongTR	0.8682	0.8893	0.9296	0.8786	95.71	99.59%
Straglr	N/A					96.86%
STRdust	0.7059	0.8460	0.8443	0.7697	94.11	99.63%

[i] Performance metrics for long-read STR genotypers on an STR-only subset of HG002 variants regions from the Genome-in-a-Bottle tandem repeats v1.0 benchmark, as measured by Truvari: precision, recall, accuracy, F1 score, and Truvari's TruScore allele similarity metric. All metrics except TruScore are only for variants with an allele size difference of ≥5 bp versus hg38. Straglr VCFs are not compatible with Truvari, and TRGT cannot use ONT data owing to a licensing restriction. Underlines indicate the best value for a metric within the sequencing technology.