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Octopus v0.7.4, tumour-only, Illumina (Chen et al. 2025)

Octopus v0.7.4, tumour-only, Illumina: Tumour-only run with the authors' recommended settings.

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Evaluations and results

2 evaluations · 14 results. Different protocols are not a single leaderboard.

Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)

Sorted by AUPRC (indel only, tumour-only, 50x tumour coverage) (higher 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	AUPRC (indel only, tumour-only, 50x tumour coverage)	AUPRC (SNV only, tumour-only, 50x tumour coverage)	F1 (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	F1 (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	False negatives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	False negatives (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	False positives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	False positives (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	Precision (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	Precision (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	Recall (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	Recall (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	True positives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	True positives (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)
Octopus v0.7.4, tumour-only, Illumina (Chen et al. 2025)Evaluation	Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b)	0.0044	Not reported	0.0096	Not reported	609	Not reported	20,809	Not reported	0.005	Not reported	0.146	Not reported	104	Not reported
Octopus v0.7.4, tumour-only, Illumina (Chen et al. 2025)Evaluation	Illumina COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7b)	Not reported	0.212	Not reported	0.403	Not reported	9,792	Not reported	80,410	Not reported	0.275	Not reported	0.757	Not reported	30,440

All 14 result rows with coverage, uncertainty and sources

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Octopus v0.7.4, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	0.0044 AUPRC (indel only, tumour-only, 50x tumour coverage) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Octopus on illumina-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Octopus', Tumor coverage '50x', Type 'Indel', column 'AUPRC'
Configuration: Octopus v0.7.4, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	0.0096 F1 (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Octopus on illumina-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Octopus', Tumor coverage '50x', Type 'Indel', column 'F1-score'
Configuration: Octopus v0.7.4, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	609 False negatives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Octopus on illumina-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Octopus', Tumor coverage '50x', Type 'Indel', column 'FN'
Configuration: Octopus v0.7.4, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	20,809 False positives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Octopus on illumina-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Octopus', Tumor coverage '50x', Type 'Indel', column 'FP'
Configuration: Octopus v0.7.4, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	0.005 Precision (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Octopus on illumina-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Octopus', Tumor coverage '50x', Type 'Indel', column 'Precision'
Configuration: Octopus v0.7.4, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	0.146 Recall (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Octopus on illumina-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Octopus', Tumor coverage '50x', Type 'Indel', column 'Recall'
Configuration: Octopus v0.7.4, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	104 True positives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Octopus on illumina-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Octopus', Tumor coverage '50x', Type 'Indel', column 'TP'
Configuration: Octopus v0.7.4, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	0.212 AUPRC (SNV only, tumour-only, 50x tumour coverage) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Octopus on illumina-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Octopus', Tumor coverage '50x', Type 'SNV', column 'AUPRC'
Configuration: Octopus v0.7.4, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	0.403 F1 (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Octopus on illumina-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Octopus', Tumor coverage '50x', Type 'SNV', column 'F1-score'
Configuration: Octopus v0.7.4, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	9,792 False negatives (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Octopus on illumina-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Octopus', Tumor coverage '50x', Type 'SNV', column 'FN'
Configuration: Octopus v0.7.4, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	80,410 False positives (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Octopus on illumina-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Octopus', Tumor coverage '50x', Type 'SNV', column 'FP'
Configuration: Octopus v0.7.4, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	0.275 Precision (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Octopus on illumina-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Octopus', Tumor coverage '50x', Type 'SNV', column 'Precision'
Configuration: Octopus v0.7.4, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	0.757 Recall (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Octopus on illumina-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Octopus', Tumor coverage '50x', Type 'SNV', column 'Recall'
Configuration: Octopus v0.7.4, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	30,440 True positives (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Octopus on illumina-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Octopus', Tumor coverage '50x', Type 'SNV', column 'TP'

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3 source records and release history

ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling · Original source · Nature Communications, published 2025-10-31; PMC12579226 full-text XML
ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines) · Original source · Supplementary Information PDF (41467_2025_64547_MOESM1_ESM.pdf) of the published article
ClairS-TO Source Data workbook · Original source · Source Data file (41467_2025_64547_MOESM6_ESM.xlsx) of the published article

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Technical metadata and extraction receipts

Stable ID: somatic-clairs-to-20261011-config-octopus-illumina

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: Octopus
version: v0.7.4
foundation model eligible: false
parameters: Tumour-only run with the authors' recommended settings (Supplementary Information command lines)
access reuse: Public open-source software and released models
source locator: Supplementary Information 'Command lines used'; Supplementary Tables 2 and 7 row labels
provenance note: Octopus as run on Illumina tumour-only data in the cited comparison.

Related records

configuration of: Octopus
system: Octopus on illumina-colo829 tumour-only Indel (Chen et al. 2025)
system: Octopus on illumina-colo829 tumour-only SNV (Chen et al. 2025)

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