Relevance of Positive-control virus detection by read depth (Tisza et al. 2026 Table S2) to "Select a DNA pathogen-identification workflow for diagnostic testing"
- Use case
- Select a DNA pathogen-identification workflow for diagnostic testing
- Assessed by
- Positive-control virus detection by read depth (Tisza et al. 2026 Table S2)
- Relevance
- Proxy evidence
- Endpoint
- Model-estimated family-level detection probability at 10 and 100 read pairs for reads from seven divergent virus genomes (75.9% to 95.6% ANI to the nearest reference), with 95% intervals
Detection of reads from four Genomoviridae (DNA viruses) and three picornaviruses at 75.9% to 95.6% ANI to the nearest reference bears on the use case's question of organisms poorly represented in the reference. It is proxy evidence: viral only, synthetic reads, family-level scoring and a developer-run comparison.
5 reviewed evaluations
- Centrifuger v1.1.1-r309 on Positive-control virus detection by read depth (Tisza et al. 2026 Table S2)
- EsViritu v1.3.1 on Positive-control virus detection by read depth (Tisza et al. 2026 Table S2)
- Kraken2 v2.17.1 on Positive-control virus detection by read depth (Tisza et al. 2026 Table S2)
- Metabuli v1.2.0 on Positive-control virus detection by read depth (Tisza et al. 2026 Table S2)
- Sylph v0.9.0 on Positive-control virus detection by read depth (Tisza et al. 2026 Table S2)
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.
40 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
Citation locations2 values
| EsViritu is a sensitive and specific profiler for viral pathogen detection and genome recovery in metagenomes rna-pathogen-20261011-tisza2026-source-supp: Supplemental Table S2 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 10.64898/2026.09.29.755457 v1, posted 2026-09-30; JATS XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Citation locations2 values
| Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) rna-pathogen-20261011-tisza2026-source-supp: Supplemental Table S2 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 10.64898/2026.09.29.755457 v1 supplementary file DC1 (755457_file02.xlsx) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison group tisza2026-virus-profilers Context-only references | EsViritu is a sensitive and specific profiler for viral pathogen detection and genome recovery in metagenomes rna-pathogen-20261011-tisza2026-source-supp: Supplemental Table S2 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 10.64898/2026.09.29.755457 v1, posted 2026-09-30; JATS XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison group tisza2026-virus-profilers Context-only references | Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) rna-pathogen-20261011-tisza2026-source-supp: Supplemental Table S2 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 10.64898/2026.09.29.755457 v1 supplementary file DC1 (755457_file02.xlsx) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison title Virus profilers on a shared Virus Pathogen Database (Tisza et al. 2026, developer benchmark) Context-only references | EsViritu is a sensitive and specific profiler for viral pathogen detection and genome recovery in metagenomes rna-pathogen-20261011-tisza2026-source-supp: Supplemental Table S2 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 10.64898/2026.09.29.755457 v1, posted 2026-09-30; JATS XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison title Virus profilers on a shared Virus Pathogen Database (Tisza et al. 2026, developer benchmark) Context-only references | Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) rna-pathogen-20261011-tisza2026-source-supp: Supplemental Table S2 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 10.64898/2026.09.29.755457 v1 supplementary file DC1 (755457_file02.xlsx) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Constraints2 values
| EsViritu is a sensitive and specific profiler for viral pathogen detection and genome recovery in metagenomes rna-pathogen-20261011-tisza2026-source-supp: Supplemental Table S2 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 10.64898/2026.09.29.755457 v1, posted 2026-09-30; JATS XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Constraints2 values
| Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) rna-pathogen-20261011-tisza2026-source-supp: Supplemental Table S2 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 10.64898/2026.09.29.755457 v1 supplementary file DC1 (755457_file02.xlsx) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Endpoint Model-estimated family-level detection probability at 10 and 100 read pairs for reads from seven divergent virus genomes (75.9% to 95.6% ANI to the nearest reference), with 95% intervals Context-only references | EsViritu is a sensitive and specific profiler for viral pathogen detection and genome recovery in metagenomes rna-pathogen-20261011-tisza2026-source-supp: Supplemental Table S2 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 10.64898/2026.09.29.755457 v1, posted 2026-09-30; JATS XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Endpoint Model-estimated family-level detection probability at 10 and 100 read pairs for reads from seven divergent virus genomes (75.9% to 95.6% ANI to the nearest reference), with 95% intervals Context-only references | Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) rna-pathogen-20261011-tisza2026-source-supp: Supplemental Table S2 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 10.64898/2026.09.29.755457 v1 supplementary file DC1 (755457_file02.xlsx) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
2 source records 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
- 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)
Technical metadata and extraction receipts
Stable ID: use-case-mapping-dna-pathogen-20261011-tisza2026-pos
- field
- links:assessed_by:rna-pathogen-20261011-tisza2026-protocol-pos
- value
- rna-pathogen-20261011-tisza2026-protocol-pos
- relevance
- proxy
- endpoint
- Model-estimated family-level detection probability at 10 and 100 read pairs for reads from seven divergent virus genomes (75.9% to 95.6% ANI to the nearest reference), with 95% intervals
- rationale
- Detection of reads from four Genomoviridae (DNA viruses) and three picornaviruses at 75.9% to 95.6% ANI to the nearest reference bears on the use case's question of organisms poorly represented in the reference. It is proxy evidence: viral only, synthetic reads, family-level scoring and a developer-run comparison.
- constraints
- Inspect every linked evaluation's source locator and preserved limitations before citing a result.; Do not combine these results with another protocol's results; datasets, databases and scoring rules differ between sources.
- limitations
- Developer benchmark: the EsViritu authors built the data, chose the comparators' parameter grids and headline settings, and ran every tool (author_reported).; Preprint (bioRxiv v1); not peer reviewed.; Synthetic reads or pathogen-free libraries only; no clinical specimens and no reference laboratory test.; All tools queried the same Virus Pathogen Database (v3.2.4b), so results compare algorithms with reference content held constant, not tools as usually deployed with their own databases.; Viruses only; no bacteria, fungi or parasites.; Results are not split by DNA or RNA genome.
- citation locators
- source id: rna-pathogen-20261011-tisza2026-source; locator: Methods 'Tools and parameters', 'Positive controls', 'Negative controls', 'Mock communities'; source id: rna-pathogen-20261011-tisza2026-source-supp; locator: Supplemental Table S2
- source locator
- rna-pathogen-20261011-tisza2026-source-supp: Supplemental Table S2
- revision
- 1
- reason
- Recorded from the 2026-10-11 pathogen-detection literature pass (data/omics/use-case-coverage-rna-pathogen-20261011-tisza2026). Independently reviewed in docs/reviews/use-cases/pathogen-use-cases-2026-10-11.md.
- comparison group
- tisza2026-virus-profilers
- comparison title
- Virus profilers on a shared Virus Pathogen Database (Tisza et al. 2026, developer benchmark)
- headline metric
- recall
- stratum label
- Positive controls (divergent genomes)
- stratum order
- 1
- review
- method: source-hash-verification; independent-cell-check; scope-review; reviewer: claude; reviewer note: Separate Claude review agent (reviewer-path), independent of the extractor; no human review claimed; date: 2026-10-11; artifact sha256: fd92099655ddefdec31d35e273b80c4b233eed395c1cfc137eaddaa4efee232b; retrieval url: https://www.biorxiv.org/content/early/2026/09/30/2026.09.29.755457.source.xml; method note: Judgement drafted by the extracting agent from the pinned preprint and workbook.; 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.
- reviewed evaluations
- rna-pathogen-20261011-tisza2026-eval-pos-centrifuger; rna-pathogen-20261011-tisza2026-eval-pos-esviritu; rna-pathogen-20261011-tisza2026-eval-pos-kraken2; rna-pathogen-20261011-tisza2026-eval-pos-metabuli; rna-pathogen-20261011-tisza2026-eval-pos-sylph
- pins
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