Centrifuger v1.1.1-r309, headline setting (Tisza et al. 2026)
Centrifuger v1.1.1-r309 at the authors' headline parameter setting, querying the EsViritu Virus Pathogen Database.
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Evaluations and results
3 evaluations · 21 results. Different protocols are not a single leaderboard.
Sorted by Bray curtis dissimilarity (RPM-based abundance profile; mean over mock communities; ANI-capped truth) (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 | Bray curtis dissimilarity (RPM-based abundance profile; mean over mock communities; ANI-capped truth) | Bray curtis dissimilarity (RPM-based abundance profile; mean over six mock communities; rank family, strict truth) | Bray curtis dissimilarity (RPM-based abundance profile; mean over six mock communities; rank genus, strict truth) | Bray curtis dissimilarity (RPM-based abundance profile; mean over six mock communities; rank species, strict truth) | Bray curtis dissimilarity (RPM-based abundance profile; mean over six mock communities; rank subspecies, strict truth) | F1 (taxon detection; mean over mock communities; ANI-capped truth) | F1 (taxon detection; mean over six mock communities; rank family, strict truth) | F1 (taxon detection; mean over six mock communities; rank genus, strict truth) | F1 (taxon detection; mean over six mock communities; rank species, strict truth) | F1 (taxon detection; mean over six mock communities; rank subspecies, strict truth) | False positive rate (percentage of individual reads falsely assigned; mean over seven negative-control libraries) | False positive rate (percentage of individual reads falsely assigned; median over seven negative-control libraries) | False positives (false species reported; maximum over seven negative-control libraries) | False positives (false species reported; median over seven negative-control libraries) | Pearson (abundance profile against truth; mean over mock communities; ANI-capped truth) | Pearson (abundance profile against truth; mean over six mock communities; rank family, strict truth) | Pearson (abundance profile against truth; mean over six mock communities; rank genus, strict truth) | Pearson (abundance profile against truth; mean over six mock communities; rank species, strict truth) | Pearson (abundance profile against truth; mean over six mock communities; rank subspecies, strict truth) | Recall (model-estimated family-level detection probability at 10 read pairs; marginal mean over seven positive-control genomes) | Recall (model-estimated family-level detection probability at 100 read pairs; marginal mean over seven positive-control genomes) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Centrifuger v1.1.1-r309, headline setting (Tisza et al. 2026)Evaluation | Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9), Six mutated virus mock communities with bacterial and human background (Tisza et al. 2026) | 0.846 | 0.615 | 0.626 | 0.639 | 0.584 | 0.247 | 0.727 | 0.648 | 0.579 | 0.613 | Not reported | Not reported | Not reported | Not reported | -0.105 | 0.321 | 0.321 | 0.304 | 0.335 | Not reported | Not reported |
| Centrifuger v1.1.1-r309, headline setting (Tisza et al. 2026)Evaluation | False positives in seven pathogen-free libraries (Tisza et al. 2026 Table S6), Seven pathogen-free negative-control read libraries (Tisza et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.000003% | 0% | 2 | 0 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Centrifuger v1.1.1-r309, headline setting (Tisza et al. 2026)Evaluation | Positive-control virus detection by read depth (Tisza et al. 2026 Table S2), Positive-control synthetic reads from seven divergent virus genomes (Tisza et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.0117 | 0.198 |
All 21 result rows with coverage, uncertainty and sources
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Centrifuger v1.1.1-r309, 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) | 0.846 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 sourcerna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 24 (base_tool 'Centrifuger', rank 'ani_capped', truth_mode 'capped'), column 'bray_curtis' (cell E24) |
| Configuration: Centrifuger v1.1.1-r309, 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) | 0.247 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 sourcerna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 24 (base_tool 'Centrifuger', rank 'ani_capped', truth_mode 'capped'), column 'F1' (cell D24) |
| Configuration: Centrifuger v1.1.1-r309, 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) | -0.105 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 sourcerna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 24 (base_tool 'Centrifuger', rank 'ani_capped', truth_mode 'capped'), column 'pearson' (cell F24) |
| Configuration: Centrifuger v1.1.1-r309, 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) | 0.615 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 sourcerna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 4 (base_tool 'Centrifuger', rank 'family', truth_mode 'strict'), column 'bray_curtis' (cell E4) |
| Configuration: Centrifuger v1.1.1-r309, 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) | 0.727 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 sourcerna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 4 (base_tool 'Centrifuger', rank 'family', truth_mode 'strict'), column 'F1' (cell D4) |
| Configuration: Centrifuger v1.1.1-r309, 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) | 0.321 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 sourcerna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 4 (base_tool 'Centrifuger', rank 'family', truth_mode 'strict'), column 'pearson' (cell F4) |
| Configuration: Centrifuger v1.1.1-r309, 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) | 0.626 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 sourcerna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 9 (base_tool 'Centrifuger', rank 'genus', truth_mode 'strict'), column 'bray_curtis' (cell E9) |
| Configuration: Centrifuger v1.1.1-r309, 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) | 0.648 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 sourcerna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 9 (base_tool 'Centrifuger', rank 'genus', truth_mode 'strict'), column 'F1' (cell D9) |
| Configuration: Centrifuger v1.1.1-r309, 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) | 0.321 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 sourcerna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 9 (base_tool 'Centrifuger', rank 'genus', truth_mode 'strict'), column 'pearson' (cell F9) |
| Configuration: Centrifuger v1.1.1-r309, 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) | 0.639 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 sourcerna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 14 (base_tool 'Centrifuger', rank 'species', truth_mode 'strict'), column 'bray_curtis' (cell E14) |
| Configuration: Centrifuger v1.1.1-r309, 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) | 0.579 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 sourcerna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 14 (base_tool 'Centrifuger', rank 'species', truth_mode 'strict'), column 'F1' (cell D14) |
| Configuration: Centrifuger v1.1.1-r309, 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) | 0.304 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 sourcerna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 14 (base_tool 'Centrifuger', rank 'species', truth_mode 'strict'), column 'pearson' (cell F14) |
| Configuration: Centrifuger v1.1.1-r309, 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) | 0.584 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 sourcerna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 19 (base_tool 'Centrifuger', rank 'subspecies', truth_mode 'strict'), column 'bray_curtis' (cell E19) |
| Configuration: Centrifuger v1.1.1-r309, 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) | 0.613 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 sourcerna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 19 (base_tool 'Centrifuger', rank 'subspecies', truth_mode 'strict'), column 'F1' (cell D19) |
| Configuration: Centrifuger v1.1.1-r309, 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) | 0.335 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 sourcerna-pathogen-20261011-tisza2026-protocol-mock Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S9, row 19 (base_tool 'Centrifuger', rank 'subspecies', truth_mode 'strict'), column 'pearson' (cell F19) |
| Configuration: Centrifuger v1.1.1-r309, 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) | 2 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 sourcerna-pathogen-20261011-tisza2026-protocol-neg Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S6, row 5 (base_tool 'Centrifuger'), column 'max_n_species' (cell F5) |
| Configuration: Centrifuger v1.1.1-r309, 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) | 0.000003% 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 sourcerna-pathogen-20261011-tisza2026-protocol-neg Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S6, row 5 (base_tool 'Centrifuger'), column 'mean_fp_pct' (cell D5) |
| Configuration: Centrifuger v1.1.1-r309, 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 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 sourcerna-pathogen-20261011-tisza2026-protocol-neg Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S6, row 5 (base_tool 'Centrifuger'), column 'median_fp_pct' (cell C5) |
| Configuration: Centrifuger v1.1.1-r309, 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 sourcerna-pathogen-20261011-tisza2026-protocol-neg Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S6, row 5 (base_tool 'Centrifuger'), column 'median_n_species' (cell E5) |
| Configuration: Centrifuger v1.1.1-r309, 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) | 0.0117 Recall (model-estimated family-level detection probability at 10 read pairs; marginal mean over seven positive-control genomes) fraction · higher Uncertainty: 95% CI 0.00495878224532846 to 0.02719564873770782. Asymptotic interval from brglm2 estimated marginal means; standard error printed 0.005072199752721945 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcerna-pathogen-20261011-tisza2026-protocol-pos Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S2, row 5 (base_tool 'Centrifuger', read_pairs 10), column 'prob' (cell C5); interval columns 'asymp.LCL' and 'asymp.UCL' |
| Configuration: Centrifuger v1.1.1-r309, 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) | 0.198 Recall (model-estimated family-level detection probability at 100 read pairs; marginal mean over seven positive-control genomes) fraction · higher Uncertainty: 95% CI 0.1247430998401599 to 0.2996024520084267. Asymptotic interval from brglm2 estimated marginal means; standard error printed 0.04452631953737853 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcerna-pathogen-20261011-tisza2026-protocol-pos Aggregation: Not reported Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S2, row 10 (base_tool 'Centrifuger', read_pairs 100), column 'prob' (cell C10); interval columns 'asymp.LCL' and 'asymp.UCL' |
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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
1 source record and release history
- EsViritu is a sensitive and specific profiler for viral pathogen detection and genome recovery in metagenomes · Original source · bioRxiv 10.64898/2026.09.29.755457 v1, posted 2026-09-30; JATS XML
Technical metadata and extraction receipts
Stable ID: rna-pathogen-20261011-tisza2026-config-centrifuger
- areas
- microbes-communities
- contexts
- research
- method types
- conventional_pipeline
- reported name
- Centrifuger v1.1.1-r309
- version
- 1.1.1-r309
- foundation model eligible
- false
- parameters
- minimum-hit-length 100, minimum score 0; database: EsViritu Virus Pathogen Database v3.2.4b (v3.2.4 with taxonomy labels taken only from the NCBI TaxDump of 2026-06-01), built into each tool's own index format
- source locator
- Methods 'Tools and parameters'; Results 'EsViritu reaches read-level sensitivity while avoiding false positives' paragraph 3 (Headline setting 'Centrifuger=minimum-hit-length:100, minimum score:0')
- access reuse
- Third-party tool run by the EsViritu authors; access not described in the source
Related records
- configuration of: Centrifuger
- system: Centrifuger v1.1.1-r309 on Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9)
- system: Centrifuger v1.1.1-r309 on False positives in seven pathogen-free libraries (Tisza et al. 2026 Table S6)
- system: Centrifuger v1.1.1-r309 on Positive-control virus detection by read depth (Tisza et al. 2026 Table S2)