| Configuration: Sylph v0.9.0, headline setting (Tisza et al. 2026) | Protocol: Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9)
Dataset: Six mutated virus mock communities with bacterial and human background (Tisza et al. 2026) | NA Bray curtis dissimilarity (RPM-based abundance profile; mean over mock communities; ANI-capped truth) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSylph v0.9.0 on Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9) rna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 28 (base_tool 'Sylph', rank 'ani_capped', truth_mode 'capped'), column 'bray_curtis' (cell E28) |
|---|
| Configuration: Sylph v0.9.0, headline setting (Tisza et al. 2026) | Protocol: Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9)
Dataset: Six mutated virus mock communities with bacterial and human background (Tisza et al. 2026) | 0.477 F1 (taxon detection; mean over mock communities; ANI-capped truth) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSylph v0.9.0 on Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9) rna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 28 (base_tool 'Sylph', rank 'ani_capped', truth_mode 'capped'), column 'F1' (cell D28) |
|---|
| Configuration: Sylph v0.9.0, headline setting (Tisza et al. 2026) | Protocol: Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9)
Dataset: Six mutated virus mock communities with bacterial and human background (Tisza et al. 2026) | NA Pearson (abundance profile against truth; mean over mock communities; ANI-capped truth) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSylph v0.9.0 on Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9) rna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 28 (base_tool 'Sylph', rank 'ani_capped', truth_mode 'capped'), column 'pearson' (cell F28) |
|---|
| Configuration: Sylph v0.9.0, headline setting (Tisza et al. 2026) | Protocol: Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9)
Dataset: Six mutated virus mock communities with bacterial and human background (Tisza et al. 2026) | NA Bray curtis dissimilarity (RPM-based abundance profile; mean over six mock communities; rank family, strict truth) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSylph v0.9.0 on Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9) rna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 8 (base_tool 'Sylph', rank 'family', truth_mode 'strict'), column 'bray_curtis' (cell E8) |
|---|
| Configuration: Sylph v0.9.0, headline setting (Tisza et al. 2026) | Protocol: Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9)
Dataset: Six mutated virus mock communities with bacterial and human background (Tisza et al. 2026) | 0.601 F1 (taxon detection; mean over six mock communities; rank family, strict truth) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSylph v0.9.0 on Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9) rna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 8 (base_tool 'Sylph', rank 'family', truth_mode 'strict'), column 'F1' (cell D8) |
|---|
| Configuration: Sylph v0.9.0, headline setting (Tisza et al. 2026) | Protocol: Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9)
Dataset: Six mutated virus mock communities with bacterial and human background (Tisza et al. 2026) | NA Pearson (abundance profile against truth; mean over six mock communities; rank family, strict truth) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSylph v0.9.0 on Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9) rna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 8 (base_tool 'Sylph', rank 'family', truth_mode 'strict'), column 'pearson' (cell F8) |
|---|
| Configuration: Sylph v0.9.0, headline setting (Tisza et al. 2026) | Protocol: Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9)
Dataset: Six mutated virus mock communities with bacterial and human background (Tisza et al. 2026) | NA Bray curtis dissimilarity (RPM-based abundance profile; mean over six mock communities; rank genus, strict truth) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSylph v0.9.0 on Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9) rna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 13 (base_tool 'Sylph', rank 'genus', truth_mode 'strict'), column 'bray_curtis' (cell E13) |
|---|
| Configuration: Sylph v0.9.0, headline setting (Tisza et al. 2026) | Protocol: Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9)
Dataset: Six mutated virus mock communities with bacterial and human background (Tisza et al. 2026) | 0.569 F1 (taxon detection; mean over six mock communities; rank genus, strict truth) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSylph v0.9.0 on Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9) rna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 13 (base_tool 'Sylph', rank 'genus', truth_mode 'strict'), column 'F1' (cell D13) |
|---|
| Configuration: Sylph v0.9.0, headline setting (Tisza et al. 2026) | Protocol: Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9)
Dataset: Six mutated virus mock communities with bacterial and human background (Tisza et al. 2026) | NA Pearson (abundance profile against truth; mean over six mock communities; rank genus, strict truth) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSylph v0.9.0 on Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9) rna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 13 (base_tool 'Sylph', rank 'genus', truth_mode 'strict'), column 'pearson' (cell F13) |
|---|
| Configuration: Sylph v0.9.0, headline setting (Tisza et al. 2026) | Protocol: Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9)
Dataset: Six mutated virus mock communities with bacterial and human background (Tisza et al. 2026) | NA Bray curtis dissimilarity (RPM-based abundance profile; mean over six mock communities; rank species, strict truth) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSylph v0.9.0 on Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9) rna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 18 (base_tool 'Sylph', rank 'species', truth_mode 'strict'), column 'bray_curtis' (cell E18) |
|---|
| Configuration: Sylph v0.9.0, headline setting (Tisza et al. 2026) | Protocol: Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9)
Dataset: Six mutated virus mock communities with bacterial and human background (Tisza et al. 2026) | 0.499 F1 (taxon detection; mean over six mock communities; rank species, strict truth) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSylph v0.9.0 on Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9) rna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 18 (base_tool 'Sylph', rank 'species', truth_mode 'strict'), column 'F1' (cell D18) |
|---|
| Configuration: Sylph v0.9.0, headline setting (Tisza et al. 2026) | Protocol: Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9)
Dataset: Six mutated virus mock communities with bacterial and human background (Tisza et al. 2026) | NA Pearson (abundance profile against truth; mean over six mock communities; rank species, strict truth) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSylph v0.9.0 on Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9) rna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 18 (base_tool 'Sylph', rank 'species', truth_mode 'strict'), column 'pearson' (cell F18) |
|---|
| Configuration: Sylph v0.9.0, headline setting (Tisza et al. 2026) | Protocol: Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9)
Dataset: Six mutated virus mock communities with bacterial and human background (Tisza et al. 2026) | NA Bray curtis dissimilarity (RPM-based abundance profile; mean over six mock communities; rank subspecies, strict truth) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSylph v0.9.0 on Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9) rna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 23 (base_tool 'Sylph', rank 'subspecies', truth_mode 'strict'), column 'bray_curtis' (cell E23) |
|---|
| Configuration: Sylph v0.9.0, headline setting (Tisza et al. 2026) | Protocol: Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9)
Dataset: Six mutated virus mock communities with bacterial and human background (Tisza et al. 2026) | 0.537 F1 (taxon detection; mean over six mock communities; rank subspecies, strict truth) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSylph v0.9.0 on Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9) rna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 23 (base_tool 'Sylph', rank 'subspecies', truth_mode 'strict'), column 'F1' (cell D23) |
|---|
| Configuration: Sylph v0.9.0, headline setting (Tisza et al. 2026) | Protocol: Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9)
Dataset: Six mutated virus mock communities with bacterial and human background (Tisza et al. 2026) | NA Pearson (abundance profile against truth; mean over six mock communities; rank subspecies, strict truth) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSylph v0.9.0 on Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9) rna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 23 (base_tool 'Sylph', rank 'subspecies', truth_mode 'strict'), column 'pearson' (cell F23) |
|---|
| Configuration: Sylph v0.9.0, headline setting (Tisza et al. 2026) | Protocol: False positives in seven pathogen-free libraries (Tisza et al. 2026 Table S6)
Dataset: Seven pathogen-free negative-control read libraries (Tisza et al. 2026) | 0 False positives (false species reported; maximum over seven negative-control libraries) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSylph v0.9.0 on False positives in seven pathogen-free libraries (Tisza et al. 2026 Table S6) rna-pathogen-20261011-tisza2026-protocol-neg Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S6, row 8 (base_tool 'Sylph'), column 'max_n_species' (cell F8) |
|---|
| Configuration: Sylph v0.9.0, headline setting (Tisza et al. 2026) | Protocol: False positives in seven pathogen-free libraries (Tisza et al. 2026 Table S6)
Dataset: Seven pathogen-free negative-control read libraries (Tisza et al. 2026) | NA% False positive rate (percentage of individual reads falsely assigned; mean over seven negative-control libraries) percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSylph v0.9.0 on False positives in seven pathogen-free libraries (Tisza et al. 2026 Table S6) rna-pathogen-20261011-tisza2026-protocol-neg Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S6, row 8 (base_tool 'Sylph'), column 'mean_fp_pct' (cell D8) |
|---|
| Configuration: Sylph v0.9.0, headline setting (Tisza et al. 2026) | Protocol: False positives in seven pathogen-free libraries (Tisza et al. 2026 Table S6)
Dataset: Seven pathogen-free negative-control read libraries (Tisza et al. 2026) | NA% False positive rate (percentage of individual reads falsely assigned; median over seven negative-control libraries) percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSylph v0.9.0 on False positives in seven pathogen-free libraries (Tisza et al. 2026 Table S6) rna-pathogen-20261011-tisza2026-protocol-neg Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S6, row 8 (base_tool 'Sylph'), column 'median_fp_pct' (cell C8) |
|---|
| Configuration: Sylph v0.9.0, headline setting (Tisza et al. 2026) | Protocol: False positives in seven pathogen-free libraries (Tisza et al. 2026 Table S6)
Dataset: Seven pathogen-free negative-control read libraries (Tisza et al. 2026) | 0 False positives (false species reported; median over seven negative-control libraries) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSylph v0.9.0 on False positives in seven pathogen-free libraries (Tisza et al. 2026 Table S6) rna-pathogen-20261011-tisza2026-protocol-neg Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S6, row 8 (base_tool 'Sylph'), column 'median_n_species' (cell E8) |
|---|
| Configuration: Sylph v0.9.0, headline setting (Tisza et al. 2026) | Protocol: Positive-control virus detection by read depth (Tisza et al. 2026 Table S2)
Dataset: Positive-control synthetic reads from seven divergent virus genomes (Tisza et al. 2026) | 0.000884 Recall (model-estimated family-level detection probability at 10 read pairs; marginal mean over seven positive-control genomes) fraction · higher Uncertainty: 95% CI 0.0002455506729957742 to 0.003174226166650207. Asymptotic interval from brglm2 estimated marginal means; standard error printed 0.0005770437158860627 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSylph v0.9.0 on Positive-control virus detection by read depth (Tisza et al. 2026 Table S2) rna-pathogen-20261011-tisza2026-protocol-pos Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S2, row 8 (base_tool 'Sylph', read_pairs 10), column 'prob' (cell C8); interval columns 'asymp.LCL' and 'asymp.UCL' |
|---|
| Configuration: Sylph v0.9.0, headline setting (Tisza et al. 2026) | Protocol: Positive-control virus detection by read depth (Tisza et al. 2026 Table S2)
Dataset: Positive-control synthetic reads from seven divergent virus genomes (Tisza et al. 2026) | 0.00347 Recall (model-estimated family-level detection probability at 100 read pairs; marginal mean over seven positive-control genomes) fraction · higher Uncertainty: 95% CI 0.001204394110956901 to 0.009960703944958654. Asymptotic interval from brglm2 estimated marginal means; standard error printed 0.001871995713381193 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSylph v0.9.0 on Positive-control virus detection by read depth (Tisza et al. 2026 Table S2) rna-pathogen-20261011-tisza2026-protocol-pos Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S2, row 13 (base_tool 'Sylph', read_pairs 100), column 'prob' (cell C13); interval columns 'asymp.LCL' and 'asymp.UCL' |
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