Relevance of Mutated virus mock-community profiling against ground truth (Tisza et al. 2026 Table S9) to "Select an RNA pathogen-detection workflow for diagnostic testing"

Stable ID: use-case-mapping-rna-pathogen-20261011-tisza2026-mock

field

links:assessed_by:rna-pathogen-20261011-tisza2026-protocol-mock

value

rna-pathogen-20261011-tisza2026-protocol-mock

relevance

proxy

endpoint

Mean F1, Bray-Curtis dissimilarity and Pearson correlation against ground truth in six mutated virus mock communities with bacterial and human background

rationale

Profiling accuracy on mock communities with mutated viruses in a large bacterial and human background bears on detecting viruses that differ from the reference amid background reads. It is proxy evidence: synthetic communities and 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the comparators' parameter grids and headline settings, and ran every tool (author_reported).; Preprint (bioRxiv v1); not peer reviewed.; Synthetic reads or pathogen-free libraries only; no clinical specimens and no reference laboratory test.; All tools queried the same Virus Pathogen Database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.; The communities draw from all 63 database families; the share of RNA viruses is not stated in the inspected text.; Under divergence-capped truth the Results say only the three one-per-family communities were scored, while Methods say all six were analysed together; the capped means may cover three communities.

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 S9

source locator

rna-pathogen-20261011-tisza2026-source-supp: Supplemental Table S9

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

f1-score

stratum label

Mutated mock communities

stratum order

3

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-mock-centrifuger; rna-pathogen-20261011-tisza2026-eval-mock-esviritu; rna-pathogen-20261011-tisza2026-eval-mock-kraken2; rna-pathogen-20261011-tisza2026-eval-mock-metabuli; rna-pathogen-20261011-tisza2026-eval-mock-sylph

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• subject: Select an RNA pathogen-detection workflow for diagnostic testing