Configuration

DeepVariant v1.10-beta 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

DeepVariant v1.10-beta GPU mode: google/deepvariant:v1.10-beta-gpu container, run_deepvariant with --model_type set to the platform.

2 evaluations · 40 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

2 evaluations · 40 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 (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)
DeepVariant v1.10-beta 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	125	196	235	289	346	Not reported	Not reported	Not reported	Not reported	Not reported	42,331	46,861	46,810	56,213	49,208	Not reported	Not reported	Not reported	Not reported	Not reported	63,386	56,509	60,245	65,320	69,633	Not reported	Not reported	Not reported	Not reported	Not reported	39	60	48	65	82	Not reported	Not reported	Not reported	Not reported	Not reported
DeepVariant v1.10-beta 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	80	99	128	126	155	Not reported	Not reported	Not reported	Not reported	Not reported	39,789	45,697	42,140	52,545	45,738	Not reported	Not reported	Not reported	Not reported	Not reported	52,412	58,852	57,350	66,953	58,773	Not reported	Not reported	Not reported	Not reported	Not reported	34	40	40	48	53

All 40 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: DeepVariant v1.10-beta 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	125 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	Independent external 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 DeepVariant v1.10-beta (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 'DeepVariant v1.10-beta (GPU mode)', read coverage 10x, column 'Total data movement IO (GB)'
Configuration: DeepVariant v1.10-beta 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	42,331 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	Independent external 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 DeepVariant v1.10-beta (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 'DeepVariant v1.10-beta (GPU mode)', read coverage 10x, column 'Average memory (MB)'
Configuration: DeepVariant v1.10-beta 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	63,386 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	Independent external 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 DeepVariant v1.10-beta (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 'DeepVariant v1.10-beta (GPU mode)', read coverage 10x, column 'Peak memory (MB)'
Configuration: DeepVariant v1.10-beta 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	39 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	Independent external 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 DeepVariant v1.10-beta (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 'DeepVariant v1.10-beta (GPU mode)', read coverage 10x, column 'Runtime (minutes)'
Configuration: DeepVariant v1.10-beta 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	196 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	Independent external 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 DeepVariant v1.10-beta (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 'DeepVariant v1.10-beta (GPU mode)', read coverage 20x, column 'Total data movement IO (GB)'
Configuration: DeepVariant v1.10-beta 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	46,861 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	Independent external 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 DeepVariant v1.10-beta (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 'DeepVariant v1.10-beta (GPU mode)', read coverage 20x, column 'Average memory (MB)'
Configuration: DeepVariant v1.10-beta 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	56,509 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	Independent external 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 DeepVariant v1.10-beta (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 'DeepVariant v1.10-beta (GPU mode)', read coverage 20x, column 'Peak memory (MB)'
Configuration: DeepVariant v1.10-beta 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	60 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	Independent external 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 DeepVariant v1.10-beta (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 'DeepVariant v1.10-beta (GPU mode)', read coverage 20x, column 'Runtime (minutes)'
Configuration: DeepVariant v1.10-beta 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	235 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	Independent external 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 DeepVariant v1.10-beta (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 'DeepVariant v1.10-beta (GPU mode)', read coverage 30x, column 'Total data movement IO (GB)'
Configuration: DeepVariant v1.10-beta 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	46,810 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	Independent external 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 DeepVariant v1.10-beta (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 'DeepVariant v1.10-beta (GPU mode)', read coverage 30x, column 'Average memory (MB)'
Configuration: DeepVariant v1.10-beta 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	60,245 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	Independent external 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 DeepVariant v1.10-beta (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 'DeepVariant v1.10-beta (GPU mode)', read coverage 30x, column 'Peak memory (MB)'
Configuration: DeepVariant v1.10-beta 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	48 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	Independent external 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 DeepVariant v1.10-beta (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 'DeepVariant v1.10-beta (GPU mode)', read coverage 30x, column 'Runtime (minutes)'
Configuration: DeepVariant v1.10-beta 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	289 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	Independent external 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 DeepVariant v1.10-beta (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 'DeepVariant v1.10-beta (GPU mode)', read coverage 40x, column 'Total data movement IO (GB)'
Configuration: DeepVariant v1.10-beta 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	56,213 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	Independent external 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 DeepVariant v1.10-beta (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 'DeepVariant v1.10-beta (GPU mode)', read coverage 40x, column 'Average memory (MB)'
Configuration: DeepVariant v1.10-beta 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	65,320 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	Independent external 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 DeepVariant v1.10-beta (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 'DeepVariant v1.10-beta (GPU mode)', read coverage 40x, column 'Peak memory (MB)'
Configuration: DeepVariant v1.10-beta 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	65 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	Independent external 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 DeepVariant v1.10-beta (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 'DeepVariant v1.10-beta (GPU mode)', read coverage 40x, column 'Runtime (minutes)'
Configuration: DeepVariant v1.10-beta 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	346 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	Independent external 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 DeepVariant v1.10-beta (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 'DeepVariant v1.10-beta (GPU mode)', read coverage 50x, column 'Total data movement IO (GB)'
Configuration: DeepVariant v1.10-beta 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	49,208 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	Independent external 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 DeepVariant v1.10-beta (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 'DeepVariant v1.10-beta (GPU mode)', read coverage 50x, column 'Average memory (MB)'
Configuration: DeepVariant v1.10-beta 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	69,633 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	Independent external 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 DeepVariant v1.10-beta (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 'DeepVariant v1.10-beta (GPU mode)', read coverage 50x, column 'Peak memory (MB)'
Configuration: DeepVariant v1.10-beta 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	82 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	Independent external 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 DeepVariant v1.10-beta (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 'DeepVariant v1.10-beta (GPU mode)', read coverage 50x, column 'Runtime (minutes)'
Configuration: DeepVariant v1.10-beta 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	80 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	Independent external 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 DeepVariant v1.10-beta (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 'DeepVariant v1.10-beta (GPU mode)', read coverage 10x, column 'Total data movement IO (GB)'
Configuration: DeepVariant v1.10-beta 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	39,789 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	Independent external 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 DeepVariant v1.10-beta (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 'DeepVariant v1.10-beta (GPU mode)', read coverage 10x, column 'Average memory (MB)'
Configuration: DeepVariant v1.10-beta 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	52,412 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	Independent external 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 DeepVariant v1.10-beta (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 'DeepVariant v1.10-beta (GPU mode)', read coverage 10x, column 'Peak memory (MB)'
Configuration: DeepVariant v1.10-beta 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	34 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	Independent external 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 DeepVariant v1.10-beta (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 'DeepVariant v1.10-beta (GPU mode)', read coverage 10x, column 'Runtime (minutes)'
Configuration: DeepVariant v1.10-beta 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	99 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	Independent external 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 DeepVariant v1.10-beta (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 'DeepVariant v1.10-beta (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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Stable ID: model-execution-20261011-config-zheng2026-deepvariant-1-10-beta-gpu

areas: dna-genomes
contexts: research
method types: supervised_machine_learning
reported name: DeepVariant v1.10-beta (GPU mode)
foundation model eligible: false
access reuse: Open-source software
protocol: google/deepvariant:v1.10-beta-gpu container, run_deepvariant with --model_type set to the platform (Supplementary Notes command).
version: v1.10-beta
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
model identity note: Results 3.1.1 and 3.1.2 call the DeepVariant runs v1.8; Supplementary Table 2 and the Supplementary Notes commands give v1.10-beta.
provenance note: google/deepvariant:v1.10-beta-gpu container, run_deepvariant with --model_type set to the platform (Supplementary Notes command).

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configuration of: DeepVariant
subject: version: DeepVariant runs (Zheng et al. 2026)
system: DeepVariant v1.10-beta (GPU mode), HG003 ONT runtime and memory (Zheng et al. 2026)
system: DeepVariant v1.10-beta (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026)

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