Recall (model-estimated family-level detection probability at 10 read pairs; marginal mean over seven positive-control genomes) of Kraken2 v2.17.1, headline setting (Tisza et al. 2026) on Positive-control synthetic reads from seven divergent virus genomes (Tisza et al. 2026)
0.0451 Recall (model-estimated family-level detection probability at 10 read pairs; marginal mean over seven positive-control genomes)
Methods
- Tested configuration
- Kraken2 v2.17.1, 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)
- Procedure
- Positive-control virus detection by read depth (Tisza et al. 2026 Table S2)
- Evaluation
- Kraken2 v2.17.1 on Positive-control virus detection by read depth (Tisza et al. 2026 Table S2)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- 95% CI 0.02256255452587475 to 0.08820897881741546. Asymptotic interval from brglm2 estimated marginal means; standard error printed 0.01575080088172684
- Evidence
- Author-reported evaluation · source checkedTisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Supplemental Table S2, row 6 (base_tool 'Kraken2', read_pairs 10), column 'prob' (cell C6); interval columns 'asymp.LCL' and 'asymp.UCL'
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.
Reproduction
- Split
- No split
- Adaptation
- Headline setting: confidence 0.5, minimum-hit-group 2
- Scoring implementation
- A detection is scored when a tool reports the genome's family. Bias-reduced logistic regression (brglm2 AS_mixed), genome as a fixed block, EsViritu as the reference tool; estimated marginal means at 10 and 100 read pairs.
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 0.04512377943813363 Individual claims | Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) Supplemental Table S2, row 6 (base_tool 'Kraken2', read_pairs 10), column 'prob' (cell C6); interval columns 'asymp.LCL' and 'asymp.UCL' Version: bioRxiv 10.64898/2026.09.29.755457 v1 supplementary file DC1 (755457_file02.xlsx) | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-11 author reported Audit detailsRe-downloaded the pinned artifact and matched its SHA-256; compared every value with a separate stdlib parser written for this review (the extractor's script was not run) and checked a stratified sample by hand against the rendered table. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
2 source records and release history
- Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Original source · bioRxiv 10.64898/2026.09.29.755457 v1 supplementary file DC1 (755457_file02.xlsx)
- 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-result-pos-kraken2-10
- metric
- recall
- metric direction
- higher
- unit
- fraction
- printed value
- 0.04512377943813363
- numeric value
- 0.04512377943813363
- metric qualifier
- model-estimated family-level detection probability at 10 read pairs; marginal mean over seven positive-control genomes
- source locator
- Supplemental Table S2, row 6 (base_tool 'Kraken2', read_pairs 10), column 'prob' (cell C6); interval columns 'asymp.LCL' and 'asymp.UCL'
- uncertainty
- type: confidence_interval; lower: 0.02256255452587475; upper: 0.08820897881741546; level: 0.95; method: analytic; source column: asymp.LCL, asymp.UCL; note: Asymptotic interval from brglm2 estimated marginal means; standard error printed 0.01575080088172684
- source anomaly
- Results 'EsViritu reaches read-level sensitivity while avoiding false positives' paragraph 4 prints detection probabilities (EsViritu 0.995, Metabuli 0.99996, Sylph 1.8 x 10^-3) and odds ratios that do not match Supplemental Tables S2 and S3; the text appears to describe a different fit. Value is the S2 marginal mean as printed.
- review
- method: source-hash-verification; deterministic-table-parse; independent-cell-check; reviewer: claude; reviewer note: Separate Claude review agent (reviewer-path), independent of the extractor; no human review claimed; date: 2026-10-11; artifact sha256: 0559022a3ff5ef5b2682e3c451eda51835c4c8d9be9dfdb1ebc9cd9295fb7701; retrieval url: https://www.biorxiv.org/content/biorxiv/early/2026/09/30/2026.09.29.755457/DC1/embed/media-1.xlsx?download=true; method note: Extracted by deterministic parse of the pinned XLSX sheet XML (extract/extract_tisza2026.py), with header and row labels asserted. printed_value is the cell text, or the shortest decimal that round-trips to the stored number; displayed spreadsheet formatting was not applied.; note: Re-downloaded the pinned artifact and matched its SHA-256; compared every value with a separate stdlib parser written for this review (the extractor's script was not run) and checked a stratified sample by hand against the rendered table.