Configuration

Clair3 v1.2.0 GPU mode (Zheng et al. 2026)

Evidence concern: excluded from comparisons

Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2

Clair3 v1.2.0 GPU mode: Clair3 v1.2.0 run with --use_gpu; parallel chunking, LongPhase phasing, in-memory haplotagging.

4 evaluations · 64 results

Overview

An explanatory profile has not yet been reviewed for this record.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

4 evaluations · 64 results. Different protocols are not a single leaderboard.

Sorted by Data io volume (Variant calling from BAM, whole run; HG003 ONT 10x) (lower is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	Data io volume (Variant calling from BAM, whole run; HG003 ONT 10x)	Data io volume (Variant calling from BAM, whole run; HG003 ONT 20x)	Data io volume (Variant calling from BAM, whole run; HG003 ONT 30x)	Data io volume (Variant calling from BAM, whole run; HG003 ONT 40x)	Data io volume (Variant calling from BAM, whole run; HG003 ONT 50x)	Data io volume (Variant calling from BAM, whole run; HG003 PacBio 10x)	Data io volume (Variant calling from BAM, whole run; HG003 PacBio 20x)	Data io volume (Variant calling from BAM, whole run; HG003 PacBio 30x)	Data io volume (Variant calling from BAM, whole run; HG003 PacBio 40x)	Data io volume (Variant calling from BAM, whole run; HG003 PacBio 50x)	Mean memory (Variant calling from BAM, whole run; HG003 ONT 10x)	Mean memory (Variant calling from BAM, whole run; HG003 ONT 20x)	Mean memory (Variant calling from BAM, whole run; HG003 ONT 30x)	Mean memory (Variant calling from BAM, whole run; HG003 ONT 40x)	Mean memory (Variant calling from BAM, whole run; HG003 ONT 50x)	Mean memory (Variant calling from BAM, whole run; HG003 PacBio 10x)	Mean memory (Variant calling from BAM, whole run; HG003 PacBio 20x)	Mean memory (Variant calling from BAM, whole run; HG003 PacBio 30x)	Mean memory (Variant calling from BAM, whole run; HG003 PacBio 40x)	Mean memory (Variant calling from BAM, whole run; HG003 PacBio 50x)	Peak memory (Variant calling from BAM, whole run; HG003 ONT 10x)	Peak memory (Variant calling from BAM, whole run; HG003 ONT 20x)	Peak memory (Variant calling from BAM, whole run; HG003 ONT 30x)	Peak memory (Variant calling from BAM, whole run; HG003 ONT 40x)	Peak memory (Variant calling from BAM, whole run; HG003 ONT 50x)	Peak memory (Variant calling from BAM, whole run; HG003 PacBio 10x)	Peak memory (Variant calling from BAM, whole run; HG003 PacBio 20x)	Peak memory (Variant calling from BAM, whole run; HG003 PacBio 30x)	Peak memory (Variant calling from BAM, whole run; HG003 PacBio 40x)	Peak memory (Variant calling from BAM, whole run; HG003 PacBio 50x)	Runtime (Clair3 GPU workflow, full-alignment calling stage; HG003 ONT 30x)	Runtime (Clair3 GPU workflow, full-alignment calling stage; HG003 ONT 50x)	Runtime (Clair3 GPU workflow, full-alignment calling stage; HG003 PacBio 30x)	Runtime (Clair3 GPU workflow, full-alignment calling stage; HG003 PacBio 50x)	Runtime (Clair3 GPU workflow, LongPhase variant phasing stage; HG003 ONT 30x)	Runtime (Clair3 GPU workflow, LongPhase variant phasing stage; HG003 ONT 50x)	Runtime (Clair3 GPU workflow, LongPhase variant phasing stage; HG003 PacBio 30x)	Runtime (Clair3 GPU workflow, LongPhase variant phasing stage; HG003 PacBio 50x)	Runtime (Clair3 GPU workflow, pileup calling stage; HG003 ONT 30x)	Runtime (Clair3 GPU workflow, pileup calling stage; HG003 ONT 50x)	Runtime (Clair3 GPU workflow, pileup calling stage; HG003 PacBio 30x)	Runtime (Clair3 GPU workflow, pileup calling stage; HG003 PacBio 50x)	Runtime (Clair3 GPU workflow, total; HG003 ONT 30x)	Runtime (Clair3 GPU workflow, total; HG003 ONT 50x)	Runtime (Clair3 GPU workflow, total; HG003 PacBio 30x)	Runtime (Clair3 GPU workflow, total; HG003 PacBio 50x)	Runtime (Clair3 GPU workflow, WhatsHap variant phasing stage (alternative to LongPhase); HG003 ONT 30x)	Runtime (Clair3 GPU workflow, WhatsHap variant phasing stage (alternative to LongPhase); HG003 ONT 50x)	Runtime (Clair3 GPU workflow, WhatsHap variant phasing stage (alternative to LongPhase); HG003 PacBio 30x)	Runtime (Clair3 GPU workflow, WhatsHap variant phasing stage (alternative to LongPhase); HG003 PacBio 50x)	Runtime (Clair3 GPU workflow, workflow control; HG003 ONT 30x)	Runtime (Clair3 GPU workflow, workflow control; HG003 ONT 50x)	Runtime (Clair3 GPU workflow, workflow control; HG003 PacBio 30x)	Runtime (Clair3 GPU workflow, workflow control; HG003 PacBio 50x)	Runtime (Variant calling from BAM, whole run; HG003 ONT 10x)	Runtime (Variant calling from BAM, whole run; HG003 ONT 20x)	Runtime (Variant calling from BAM, whole run; HG003 ONT 30x)	Runtime (Variant calling from BAM, whole run; HG003 ONT 40x)	Runtime (Variant calling from BAM, whole run; HG003 ONT 50x)	Runtime (Variant calling from BAM, whole run; HG003 PacBio 10x)	Runtime (Variant calling from BAM, whole run; HG003 PacBio 20x)	Runtime (Variant calling from BAM, whole run; HG003 PacBio 30x)	Runtime (Variant calling from BAM, whole run; HG003 PacBio 40x)	Runtime (Variant calling from BAM, whole run; HG003 PacBio 50x)
Clair3 v1.2.0 GPU mode (Zheng et al. 2026)Evaluation	HG003 ONT WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2), GIAB HG003 whole genome, ONT R10.4.1 5 kHz (EPI2ME giab-2025.01), subsampled to 10x-50x	137	175	222	263	307	Not reported	Not reported	Not reported	Not reported	Not reported	10,180	6,803	10,189	6,260	8,096	Not reported	Not reported	Not reported	Not reported	Not reported	45,935	56,643	57,901	62,871	63,174	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	22	16	17	18	20	Not reported	Not reported	Not reported	Not reported	Not reported
Clair3 v1.2.0 GPU mode (Zheng et al. 2026)Evaluation	HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2), GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	Not reported	Not reported	Not reported	Not reported	Not reported	88	98	128	125	139	Not reported	Not reported	Not reported	Not reported	Not reported	6,781	5,758	8,034	7,985	5,489	Not reported	Not reported	Not reported	Not reported	Not reported	41,832	52,578	49,319	46,024	55,095	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	14	13	12	12	12
Clair3 v1.2.0 GPU mode (Zheng et al. 2026)Evaluation	Clair3 GPU workflow stage runtimes on HG003 ONT and PacBio WGS (Zheng et al. 2026 Supplementary Table 1), GIAB HG003 whole genome, ONT R10.4.1 5 kHz (EPI2ME giab-2025.01), subsampled to 10x-50x	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	396	538	Not reported	Not reported	72	93	Not reported	Not reported	500	606	Not reported	Not reported	1056	1259	Not reported	Not reported	723	801	Not reported	Not reported	87	22	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Clair3 v1.2.0 GPU mode (Zheng et al. 2026)Evaluation	Clair3 GPU workflow stage runtimes on HG003 ONT and PacBio WGS (Zheng et al. 2026 Supplementary Table 1), GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	235	282	Not reported	Not reported	42	67	Not reported	Not reported	359	357	Not reported	Not reported	706	739	Not reported	Not reported	653	826	Not reported	Not reported	70	33	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported

All 64 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 ONT WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, ONT R10.4.1 5 kHz (EPI2ME giab-2025.01), subsampled to 10x-50x	137 Data io volume (Variant calling from BAM, whole run; HG003 ONT 10x) gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2 Methods, coverage and source Clair3 v1.2.0 (GPU mode), HG003 ONT runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-ont Aggregation: Not reported Accelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 2 (image, page 2), sample 'HG003 WGS', platform 'ONT r10.4.1 5kHz', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 10x, column 'Total data movement IO (GB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 ONT WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, ONT R10.4.1 5 kHz (EPI2ME giab-2025.01), subsampled to 10x-50x	10,180 Mean memory (Variant calling from BAM, whole run; HG003 ONT 10x) megabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2 Methods, coverage and source Clair3 v1.2.0 (GPU mode), HG003 ONT runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-ont Aggregation: Not reported Accelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 2 (image, page 2), sample 'HG003 WGS', platform 'ONT r10.4.1 5kHz', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 10x, column 'Average memory (MB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 ONT WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, ONT R10.4.1 5 kHz (EPI2ME giab-2025.01), subsampled to 10x-50x	45,935 Peak memory (Variant calling from BAM, whole run; HG003 ONT 10x) megabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2 Methods, coverage and source Clair3 v1.2.0 (GPU mode), HG003 ONT runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-ont Aggregation: Not reported Accelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 2 (image, page 2), sample 'HG003 WGS', platform 'ONT r10.4.1 5kHz', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 10x, column 'Peak memory (MB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 ONT WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, ONT R10.4.1 5 kHz (EPI2ME giab-2025.01), subsampled to 10x-50x	22 Runtime (Variant calling from BAM, whole run; HG003 ONT 10x) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2 Methods, coverage and source Clair3 v1.2.0 (GPU mode), HG003 ONT runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-ont Aggregation: Not reported Accelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 2 (image, page 2), sample 'HG003 WGS', platform 'ONT r10.4.1 5kHz', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 10x, column 'Runtime (minutes)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 ONT WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, ONT R10.4.1 5 kHz (EPI2ME giab-2025.01), subsampled to 10x-50x	175 Data io volume (Variant calling from BAM, whole run; HG003 ONT 20x) gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2 Methods, coverage and source Clair3 v1.2.0 (GPU mode), HG003 ONT runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-ont Aggregation: Not reported Accelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 2 (image, page 2), sample 'HG003 WGS', platform 'ONT r10.4.1 5kHz', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 20x, column 'Total data movement IO (GB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 ONT WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, ONT R10.4.1 5 kHz (EPI2ME giab-2025.01), subsampled to 10x-50x	6,803 Mean memory (Variant calling from BAM, whole run; HG003 ONT 20x) megabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2 Methods, coverage and source Clair3 v1.2.0 (GPU mode), HG003 ONT runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-ont Aggregation: Not reported Accelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 2 (image, page 2), sample 'HG003 WGS', platform 'ONT r10.4.1 5kHz', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 20x, column 'Average memory (MB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 ONT WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, ONT R10.4.1 5 kHz (EPI2ME giab-2025.01), subsampled to 10x-50x	56,643 Peak memory (Variant calling from BAM, whole run; HG003 ONT 20x) megabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2 Methods, coverage and source Clair3 v1.2.0 (GPU mode), HG003 ONT runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-ont Aggregation: Not reported Accelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 2 (image, page 2), sample 'HG003 WGS', platform 'ONT r10.4.1 5kHz', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 20x, column 'Peak memory (MB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 ONT WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, ONT R10.4.1 5 kHz (EPI2ME giab-2025.01), subsampled to 10x-50x	16 Runtime (Variant calling from BAM, whole run; HG003 ONT 20x) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2 Methods, coverage and source Clair3 v1.2.0 (GPU mode), HG003 ONT runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-ont Aggregation: Not reported Accelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 2 (image, page 2), sample 'HG003 WGS', platform 'ONT r10.4.1 5kHz', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 20x, column 'Runtime (minutes)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 ONT WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, ONT R10.4.1 5 kHz (EPI2ME giab-2025.01), subsampled to 10x-50x	222 Data io volume (Variant calling from BAM, whole run; HG003 ONT 30x) gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2 Methods, coverage and source Clair3 v1.2.0 (GPU mode), HG003 ONT runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-ont Aggregation: Not reported Accelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 2 (image, page 2), sample 'HG003 WGS', platform 'ONT r10.4.1 5kHz', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 30x, column 'Total data movement IO (GB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 ONT WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, ONT R10.4.1 5 kHz (EPI2ME giab-2025.01), subsampled to 10x-50x	10,189 Mean memory (Variant calling from BAM, whole run; HG003 ONT 30x) megabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2 Methods, coverage and source Clair3 v1.2.0 (GPU mode), HG003 ONT runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-ont Aggregation: Not reported Accelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 2 (image, page 2), sample 'HG003 WGS', platform 'ONT r10.4.1 5kHz', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 30x, column 'Average memory (MB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 ONT WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, ONT R10.4.1 5 kHz (EPI2ME giab-2025.01), subsampled to 10x-50x	57,901 Peak memory (Variant calling from BAM, whole run; HG003 ONT 30x) megabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2 Methods, coverage and source Clair3 v1.2.0 (GPU mode), HG003 ONT runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-ont Aggregation: Not reported Accelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 2 (image, page 2), sample 'HG003 WGS', platform 'ONT r10.4.1 5kHz', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 30x, column 'Peak memory (MB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 ONT WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, ONT R10.4.1 5 kHz (EPI2ME giab-2025.01), subsampled to 10x-50x	17 Runtime (Variant calling from BAM, whole run; HG003 ONT 30x) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2 Methods, coverage and source Clair3 v1.2.0 (GPU mode), HG003 ONT runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-ont Aggregation: Not reported Accelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 2 (image, page 2), sample 'HG003 WGS', platform 'ONT r10.4.1 5kHz', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 30x, column 'Runtime (minutes)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 ONT WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, ONT R10.4.1 5 kHz (EPI2ME giab-2025.01), subsampled to 10x-50x	263 Data io volume (Variant calling from BAM, whole run; HG003 ONT 40x) gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2 Methods, coverage and source Clair3 v1.2.0 (GPU mode), HG003 ONT runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-ont Aggregation: Not reported Accelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 2 (image, page 2), sample 'HG003 WGS', platform 'ONT r10.4.1 5kHz', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 40x, column 'Total data movement IO (GB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 ONT WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, ONT R10.4.1 5 kHz (EPI2ME giab-2025.01), subsampled to 10x-50x	6,260 Mean memory (Variant calling from BAM, whole run; HG003 ONT 40x) megabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2 Methods, coverage and source Clair3 v1.2.0 (GPU mode), HG003 ONT runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-ont Aggregation: Not reported Accelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 2 (image, page 2), sample 'HG003 WGS', platform 'ONT r10.4.1 5kHz', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 40x, column 'Average memory (MB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 ONT WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, ONT R10.4.1 5 kHz (EPI2ME giab-2025.01), subsampled to 10x-50x	62,871 Peak memory (Variant calling from BAM, whole run; HG003 ONT 40x) megabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2 Methods, coverage and source Clair3 v1.2.0 (GPU mode), HG003 ONT runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-ont Aggregation: Not reported Accelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 2 (image, page 2), sample 'HG003 WGS', platform 'ONT r10.4.1 5kHz', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 40x, column 'Peak memory (MB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 ONT WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, ONT R10.4.1 5 kHz (EPI2ME giab-2025.01), subsampled to 10x-50x	18 Runtime (Variant calling from BAM, whole run; HG003 ONT 40x) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2 Methods, coverage and source Clair3 v1.2.0 (GPU mode), HG003 ONT runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-ont Aggregation: Not reported Accelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 2 (image, page 2), sample 'HG003 WGS', platform 'ONT r10.4.1 5kHz', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 40x, column 'Runtime (minutes)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 ONT WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, ONT R10.4.1 5 kHz (EPI2ME giab-2025.01), subsampled to 10x-50x	307 Data io volume (Variant calling from BAM, whole run; HG003 ONT 50x) gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2 Methods, coverage and source Clair3 v1.2.0 (GPU mode), HG003 ONT runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-ont Aggregation: Not reported Accelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 2 (image, page 2), sample 'HG003 WGS', platform 'ONT r10.4.1 5kHz', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 50x, column 'Total data movement IO (GB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 ONT WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, ONT R10.4.1 5 kHz (EPI2ME giab-2025.01), subsampled to 10x-50x	8,096 Mean memory (Variant calling from BAM, whole run; HG003 ONT 50x) megabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2 Methods, coverage and source Clair3 v1.2.0 (GPU mode), HG003 ONT runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-ont Aggregation: Not reported Accelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 2 (image, page 2), sample 'HG003 WGS', platform 'ONT r10.4.1 5kHz', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 50x, column 'Average memory (MB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 ONT WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, ONT R10.4.1 5 kHz (EPI2ME giab-2025.01), subsampled to 10x-50x	63,174 Peak memory (Variant calling from BAM, whole run; HG003 ONT 50x) megabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2 Methods, coverage and source Clair3 v1.2.0 (GPU mode), HG003 ONT runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-ont Aggregation: Not reported Accelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 2 (image, page 2), sample 'HG003 WGS', platform 'ONT r10.4.1 5kHz', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 50x, column 'Peak memory (MB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 ONT WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, ONT R10.4.1 5 kHz (EPI2ME giab-2025.01), subsampled to 10x-50x	20 Runtime (Variant calling from BAM, whole run; HG003 ONT 50x) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2 Methods, coverage and source Clair3 v1.2.0 (GPU mode), HG003 ONT runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-ont Aggregation: Not reported Accelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 2 (image, page 2), sample 'HG003 WGS', platform 'ONT r10.4.1 5kHz', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 50x, column 'Runtime (minutes)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	88 Data io volume (Variant calling from BAM, whole run; HG003 PacBio 10x) gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2 Methods, coverage and source Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-pacbio Aggregation: Not reported Accelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 2 (image, page 2), sample 'HG003 WGS', platform 'PacBio Revio', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 10x, column 'Total data movement IO (GB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	6,781 Mean memory (Variant calling from BAM, whole run; HG003 PacBio 10x) megabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2 Methods, coverage and source Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-pacbio Aggregation: Not reported Accelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 2 (image, page 2), sample 'HG003 WGS', platform 'PacBio Revio', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 10x, column 'Average memory (MB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	41,832 Peak memory (Variant calling from BAM, whole run; HG003 PacBio 10x) megabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2 Methods, coverage and source Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-pacbio Aggregation: Not reported Accelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 2 (image, page 2), sample 'HG003 WGS', platform 'PacBio Revio', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 10x, column 'Peak memory (MB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	14 Runtime (Variant calling from BAM, whole run; HG003 PacBio 10x) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2 Methods, coverage and source Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-pacbio Aggregation: Not reported Accelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 2 (image, page 2), sample 'HG003 WGS', platform 'PacBio Revio', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 10x, column 'Runtime (minutes)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	98 Data io volume (Variant calling from BAM, whole run; HG003 PacBio 20x) gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2 Methods, coverage and source Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-pacbio Aggregation: Not reported Accelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 2 (image, page 2), sample 'HG003 WGS', platform 'PacBio Revio', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 20x, column 'Total data movement IO (GB)'

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Accelerated long-read variant calling with Clair3 for whole-genome sequencing · Original source · Bioinformatics 42(5), published 2026-04-10; PMC13141153 full-text XML
Accelerated long-read variant calling with Clair3: Supplementary Data · Original source · btag181_supplementary_data.pdf from the Europe PMC supplementary files of PMC13141153

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Technical metadata and extraction receipts

Stable ID: model-execution-20261011-config-zheng2026-clair3-1-2-0-gpu

areas: dna-genomes
contexts: research
method types: supervised_machine_learning
reported name: Clair3 v1.2.0 (GPU mode)
foundation model eligible: false
access reuse: Open-source software
protocol: Clair3 v1.2.0 run with --use_gpu (Supplementary Notes command); parallel chunking, LongPhase phasing, in-memory haplotagging.
version: v1.2.0
hardware: description: Not stated in Supplementary Table 2. Methods 'Computational performance' say the GPU version was benchmarked with other callers on an NVIDIA GeForce RTX 4090 with two 12-core Intel Xeon Silver 4116 processors; Results 3.1.1 and 3.1.2 give the Figure 2a runs as a Linux system with one RTX 4090 and 32 CPU threads; Supplementary Figure 2 says Clair3 used one NVIDIA 4090 GPU.
source locator: Supplementary Table 2 caller labels; Supplementary Notes command lines
provenance note: Clair3 v1.2.0 run with --use_gpu (Supplementary Notes command); parallel chunking, LongPhase phasing, in-memory haplotagging.

Related records

configuration of: Clair3
system: Clair3 v1.2.0 GPU stage runtimes, HG003 ONT (Zheng et al. 2026)
system: Clair3 v1.2.0 GPU stage runtimes, HG003 PacBio (Zheng et al. 2026)
system: Clair3 v1.2.0 (GPU mode), HG003 ONT runtime and memory (Zheng et al. 2026)
system: Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026)

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