Evidence claim

Evidence summary: DNA pathogen identification workflows

Summary of Select a DNA pathogen-identification workflow for diagnostic testing

Most workflow comparisons in the reviewed evidence use mock communities, constructed metagenomes or simulated sequences. Two compare workflows on patient specimens, and in both the reference standard draws partly on sequencing: in Hu et al. 2026 only the culture comparison is independent of the sequencing results, and in Huang et al. 2026 the reference was built mainly from BALF mNGS and the conventional tests that are themselves scored. Both are author-reported and have co-authors from sequencing companies (Genskey Medical Technology for Hu; Geneplus-Beijing, which supplies the targeted assay's probes, for Huang). For the Karius plasma cell-free DNA assay, the developers report 93.7% (59 of 63) agreement with initial blood culture in a sepsis-alert cohort, and blood culture does not detect every infection. A prospective study in children and young adults with high-risk leukaemia, with Karius taking part in sample processing and analysis, found every blood-culture organism in 81.3% (65 of 80) of evaluable bloodstream infection episodes on the day of or after onset and in 51.9% (42 of 81) during the three days before; 82.7% (134 of 162) of control samples from patients without fever or infection had no bacterium or yeast detected. In 62 bronchoalveolar lavage specimens (Hu et al. 2026), a short-read MGI workflow and a host-depleted nanopore workflow both had 95.2% positive agreement with culture but 44.6% and 46.4% negative agreement, because they found organisms culture did not; against a composite reference that adds organisms found by both workflows, positive agreement was 93.3% and 90.7%. In 122 intensive-care patients with pneumonia-associated sepsis (Huang et al. 2026), a targeted probe-capture assay on plasma had 63.46% sensitivity against the reference diagnosis, against 35.58% for untargeted blood mNGS, 49.04% for conventional tests and 9.62% for blood culture, with specificity of 44.44% and 61.11% for the two blood sequencing assays. In mock communities (Portik et al. 2022), Kraken2 and Bracken called 44 to 204 absent species at a 0.001% read threshold (precision 0.05 to 0.21), while long-read MEGAN-LR and BugSeq-V2 called 0 to 2; the first author is a PacBio employee. In seven pathogen-free libraries scored against one shared virus database by the EsViritu developers (preprint), the median number of false virus species was 0 for EsViritu, Centrifuger and Sylph, 6 for Kraken2 and 18 for Metabuli. For M. tuberculosis reads in constructed metagenomes (Hall and Coin 2024), kraken with its standard database classified 0.07 to 0.74 of the M. tuberculosis reads as M. tuberculosis, against 0.97 to 0.995 with a Mycobacterium database. Two papers by the developers of trained classifiers compare them with the baseline tools, on simulated or isolate-derived data rather than clinical specimens. On simulated 1,500-nt genome fragments (Mock et al. 2022, BERTax), Kraken2 and minimap2 assigned a superkingdom to 76.11% and 75.59% of fragments, with 99.82% and 99.95% accuracy on the fragments they assigned, when relatives were in the reference, and to 21.56% and 19.88% with 90.71% and 94.42% accuracy when each fragment's genus was absent from it; BERTax assigned every fragment, with 94.78% and 88.95% accuracy in the two settings. On in silico mixtures of nanopore isolate reads from species absent from the reference (Peres da Silva et al. 2024, MetageNN), MetageNN assigned a genus to 93.26% of reads on average across 30 mixtures, against 64.90% for Kraken2 and 53.06% for MEGAN-LR (on minimap2 alignments); MMseqs2, a reference-based tool not in the baseline, assigned 85.49%. These shares count reads assigned, not reads assigned correctly. Each study used its own reference database and reporting rules, and none of these results is clinical validation.

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Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Claimed field summary Context-only references	Karius 2019 plasma microbial cfDNA positive agreement with initial blood culture source Original source ↗ amp-20261007-dna-pathogens-source: result amp-20261007-dna-pathogens-result; dna-pathogen-20261009-source-portik2022: Table 4; dna-pathogen-20261009-source-hall2024: Tables 5-8; dna-pathogen-20261011-wolf2026-source: Tables 2 and 3; dna-pathogen-20261011-hu2026-source: Table 2; dna-pathogen-20261011-huang2026-source: Table 2; rna-pathogen-20261011-tisza2026-source-supp: Supplemental Table S6; dna-pathogen-20261012-bertax-source: Materials and Methods 'Preparing Data for Fine-Tuning' (1,500-nt fragments; closely and distantly related selection); dna-pathogen-20261012-bertax-source-si: SI Table S2 (superkingdom acc. and prop.); dna-pathogen-20261012-metagenn-source: Results 'Read classification results' paragraph 1 and the pseudo-mock 'Experimental setup' paragraph Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Blauwkamp et al., Nature Microbiology 4, 663–674 (2019) Retrieved: 2026-10-07T12:27:21.172039+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `3256a8fc4624958df4b1c7bb84632c7021240cf9471e558b625c149827a024ba` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field summary Context-only references	Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data Original source ↗ amp-20261007-dna-pathogens-source: result amp-20261007-dna-pathogens-result; dna-pathogen-20261009-source-portik2022: Table 4; dna-pathogen-20261009-source-hall2024: Tables 5-8; dna-pathogen-20261011-wolf2026-source: Tables 2 and 3; dna-pathogen-20261011-hu2026-source: Table 2; dna-pathogen-20261011-huang2026-source: Table 2; rna-pathogen-20261011-tisza2026-source-supp: Supplemental Table S6; dna-pathogen-20261012-bertax-source: Materials and Methods 'Preparing Data for Fine-Tuning' (1,500-nt fragments; closely and distantly related selection); dna-pathogen-20261012-bertax-source-si: SI Table S2 (superkingdom acc. and prop.); dna-pathogen-20261012-metagenn-source: Results 'Read classification results' paragraph 1 and the pseudo-mock 'Experimental setup' paragraph Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML Retrieved: 2026-10-09T19:55:15Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `ea3c34a01222d5c5203c52a85a700b7dae5cccd6f48e6d50808d5abbd6385554` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field summary Context-only references	Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets Original source ↗ amp-20261007-dna-pathogens-source: result amp-20261007-dna-pathogens-result; dna-pathogen-20261009-source-portik2022: Table 4; dna-pathogen-20261009-source-hall2024: Tables 5-8; dna-pathogen-20261011-wolf2026-source: Tables 2 and 3; dna-pathogen-20261011-hu2026-source: Table 2; dna-pathogen-20261011-huang2026-source: Table 2; rna-pathogen-20261011-tisza2026-source-supp: Supplemental Table S6; dna-pathogen-20261012-bertax-source: Materials and Methods 'Preparing Data for Fine-Tuning' (1,500-nt fragments; closely and distantly related selection); dna-pathogen-20261012-bertax-source-si: SI Table S2 (superkingdom acc. and prop.); dna-pathogen-20261012-metagenn-source: Results 'Read classification results' paragraph 1 and the pseudo-mock 'Experimental setup' paragraph Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML Retrieved: 2026-10-09T19:45:04Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `42cf6834ec87e149752176a65247f3aab9873f7b215037a195175a8a3113c1fe` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field summary Context-only references	Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy Original source ↗ amp-20261007-dna-pathogens-source: result amp-20261007-dna-pathogens-result; dna-pathogen-20261009-source-portik2022: Table 4; dna-pathogen-20261009-source-hall2024: Tables 5-8; dna-pathogen-20261011-wolf2026-source: Tables 2 and 3; dna-pathogen-20261011-hu2026-source: Table 2; dna-pathogen-20261011-huang2026-source: Table 2; rna-pathogen-20261011-tisza2026-source-supp: Supplemental Table S6; dna-pathogen-20261012-bertax-source: Materials and Methods 'Preparing Data for Fine-Tuning' (1,500-nt fragments; closely and distantly related selection); dna-pathogen-20261012-bertax-source-si: SI Table S2 (superkingdom acc. and prop.); dna-pathogen-20261012-metagenn-source: Results 'Read classification results' paragraph 1 and the pseudo-mock 'Experimental setup' paragraph Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Microbiology Spectrum 14(7):e03993-25, published 2026-06-03; PMC13339908 full-text XML Retrieved: 2026-10-11T21:37:24Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `555995fd870d878dd0e6c112064bbf1d2535a1cb1af17f70570ecc11774caa2d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field summary Context-only references	Blood-based targeted sequencing of microbial cell-free DNA in severe pneumonia-associated sepsis Original source ↗ amp-20261007-dna-pathogens-source: result amp-20261007-dna-pathogens-result; dna-pathogen-20261009-source-portik2022: Table 4; dna-pathogen-20261009-source-hall2024: Tables 5-8; dna-pathogen-20261011-wolf2026-source: Tables 2 and 3; dna-pathogen-20261011-hu2026-source: Table 2; dna-pathogen-20261011-huang2026-source: Table 2; rna-pathogen-20261011-tisza2026-source-supp: Supplemental Table S6; dna-pathogen-20261012-bertax-source: Materials and Methods 'Preparing Data for Fine-Tuning' (1,500-nt fragments; closely and distantly related selection); dna-pathogen-20261012-bertax-source-si: SI Table S2 (superkingdom acc. and prop.); dna-pathogen-20261012-metagenn-source: Results 'Read classification results' paragraph 1 and the pseudo-mock 'Experimental setup' paragraph Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Respiratory Research 27:357, published 2026-06-24; PMC13584460 full-text XML Retrieved: 2026-10-11T22:07:38Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `79b237d733d9ad3af33722c30013afb0539adf03098ca1e1c2f18344bcc4a67d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field summary Context-only references	Predicting bloodstream infection by plasma cell-free metagenomic sequencing: a prospective cohort study Original source ↗ amp-20261007-dna-pathogens-source: result amp-20261007-dna-pathogens-result; dna-pathogen-20261009-source-portik2022: Table 4; dna-pathogen-20261009-source-hall2024: Tables 5-8; dna-pathogen-20261011-wolf2026-source: Tables 2 and 3; dna-pathogen-20261011-hu2026-source: Table 2; dna-pathogen-20261011-huang2026-source: Table 2; rna-pathogen-20261011-tisza2026-source-supp: Supplemental Table S6; dna-pathogen-20261012-bertax-source: Materials and Methods 'Preparing Data for Fine-Tuning' (1,500-nt fragments; closely and distantly related selection); dna-pathogen-20261012-bertax-source-si: SI Table S2 (superkingdom acc. and prop.); dna-pathogen-20261012-metagenn-source: Results 'Read classification results' paragraph 1 and the pseudo-mock 'Experimental setup' paragraph Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: The Lancet Microbe 7:101312, published online 2026-03-02; PMC13154368 full-text XML (author manuscript) Retrieved: 2026-10-11T22:07:34Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `0f6905d0a0c9ace686bcc61970c711558ccf530b5c31f882607a305f8b5ca689` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field summary Context-only references	Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks Original source ↗ amp-20261007-dna-pathogens-source: result amp-20261007-dna-pathogens-result; dna-pathogen-20261009-source-portik2022: Table 4; dna-pathogen-20261009-source-hall2024: Tables 5-8; dna-pathogen-20261011-wolf2026-source: Tables 2 and 3; dna-pathogen-20261011-hu2026-source: Table 2; dna-pathogen-20261011-huang2026-source: Table 2; rna-pathogen-20261011-tisza2026-source-supp: Supplemental Table S6; dna-pathogen-20261012-bertax-source: Materials and Methods 'Preparing Data for Fine-Tuning' (1,500-nt fragments; closely and distantly related selection); dna-pathogen-20261012-bertax-source-si: SI Table S2 (superkingdom acc. and prop.); dna-pathogen-20261012-metagenn-source: Results 'Read classification results' paragraph 1 and the pseudo-mock 'Experimental setup' paragraph Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PNAS 119(35):e2122636119, published 2022-08-26; PMC9436379 full-text XML Retrieved: 2026-10-12T20:51:54Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `c0bb2f1bba8680b300076292389b39346ae58bea4bdf28647dd9462333b3bcd7` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field summary Context-only references	BERTax SI Appendix (pnas.2122636119.sapp.pdf) Original source ↗ amp-20261007-dna-pathogens-source: result amp-20261007-dna-pathogens-result; dna-pathogen-20261009-source-portik2022: Table 4; dna-pathogen-20261009-source-hall2024: Tables 5-8; dna-pathogen-20261011-wolf2026-source: Tables 2 and 3; dna-pathogen-20261011-hu2026-source: Table 2; dna-pathogen-20261011-huang2026-source: Table 2; rna-pathogen-20261011-tisza2026-source-supp: Supplemental Table S6; dna-pathogen-20261012-bertax-source: Materials and Methods 'Preparing Data for Fine-Tuning' (1,500-nt fragments; closely and distantly related selection); dna-pathogen-20261012-bertax-source-si: SI Table S2 (superkingdom acc. and prop.); dna-pathogen-20261012-metagenn-source: Results 'Read classification results' paragraph 1 and the pseudo-mock 'Experimental setup' paragraph Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: SI Appendix as distributed with PMC9436379 (member pnas.2122636119.sapp.pdf of the Europe PMC supplementaryFiles ZIP) Retrieved: 2026-10-12T20:55:54Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `89a2f86f66cbb2ff17886d413cd89577285086fedd1009e1d9daf87b29fbc1c0` Hash scope: SHA-256 of the PDF member, not of the ZIP (the ZIP is rebuilt per request) Inspected artifact
Claimed field summary Context-only references	MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes Original source ↗ amp-20261007-dna-pathogens-source: result amp-20261007-dna-pathogens-result; dna-pathogen-20261009-source-portik2022: Table 4; dna-pathogen-20261009-source-hall2024: Tables 5-8; dna-pathogen-20261011-wolf2026-source: Tables 2 and 3; dna-pathogen-20261011-hu2026-source: Table 2; dna-pathogen-20261011-huang2026-source: Table 2; rna-pathogen-20261011-tisza2026-source-supp: Supplemental Table S6; dna-pathogen-20261012-bertax-source: Materials and Methods 'Preparing Data for Fine-Tuning' (1,500-nt fragments; closely and distantly related selection); dna-pathogen-20261012-bertax-source-si: SI Table S2 (superkingdom acc. and prop.); dna-pathogen-20261012-metagenn-source: Results 'Read classification results' paragraph 1 and the pseudo-mock 'Experimental setup' paragraph Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML Retrieved: 2026-10-12T20:50:20Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `ac4b137508d295d5e04e9be263bef40bdcf2c494e096407e5896611194f14e12` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field summary Context-only references	EsViritu is a sensitive and specific profiler for viral pathogen detection and genome recovery in metagenomes Original source ↗ amp-20261007-dna-pathogens-source: result amp-20261007-dna-pathogens-result; dna-pathogen-20261009-source-portik2022: Table 4; dna-pathogen-20261009-source-hall2024: Tables 5-8; dna-pathogen-20261011-wolf2026-source: Tables 2 and 3; dna-pathogen-20261011-hu2026-source: Table 2; dna-pathogen-20261011-huang2026-source: Table 2; rna-pathogen-20261011-tisza2026-source-supp: Supplemental Table S6; dna-pathogen-20261012-bertax-source: Materials and Methods 'Preparing Data for Fine-Tuning' (1,500-nt fragments; closely and distantly related selection); dna-pathogen-20261012-bertax-source-si: SI Table S2 (superkingdom acc. and prop.); dna-pathogen-20261012-metagenn-source: Results 'Read classification results' paragraph 1 and the pseudo-mock 'Experimental setup' paragraph 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 Retrieved: 2026-10-11T21:39:50Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `fd92099655ddefdec31d35e273b80c4b233eed395c1cfc137eaddaa4efee232b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

11 source records and release history

Karius 2019 plasma microbial cfDNA positive agreement with initial blood culture source · Original source · Blauwkamp et al., Nature Microbiology 4, 663–674 (2019)
Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Original source · GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML
Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Original source · BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML
Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy · Original source · Microbiology Spectrum 14(7):e03993-25, published 2026-06-03; PMC13339908 full-text XML
Blood-based targeted sequencing of microbial cell-free DNA in severe pneumonia-associated sepsis · Original source · Respiratory Research 27:357, published 2026-06-24; PMC13584460 full-text XML
Predicting bloodstream infection by plasma cell-free metagenomic sequencing: a prospective cohort study · Original source · The Lancet Microbe 7:101312, published online 2026-03-02; PMC13154368 full-text XML (author manuscript)
Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks · Original source · PNAS 119(35):e2122636119, published 2022-08-26; PMC9436379 full-text XML
BERTax SI Appendix (pnas.2122636119.sapp.pdf) · Original source · SI Appendix as distributed with PMC9436379 (member pnas.2122636119.sapp.pdf of the Europe PMC supplementaryFiles ZIP)
MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes · Original source · BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML
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)

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Stable ID: use-case-summary-diagnostic-dna-pathogen-identification

field: summary
value: Most workflow comparisons in the reviewed evidence use mock communities, constructed metagenomes or simulated sequences. Two compare workflows on patient specimens, and in both the reference standard draws partly on sequencing: in Hu et al. 2026 only the culture comparison is independent of the sequencing results, and in Huang et al. 2026 the reference was built mainly from BALF mNGS and the conventional tests that are themselves scored. Both are author-reported and have co-authors from sequencing companies (Genskey Medical Technology for Hu; Geneplus-Beijing, which supplies the targeted assay's probes, for Huang). For the Karius plasma cell-free DNA assay, the developers report 93.7% (59 of 63) agreement with initial blood culture in a sepsis-alert cohort, and blood culture does not detect every infection. A prospective study in children and young adults with high-risk leukaemia, with Karius taking part in sample processing and analysis, found every blood-culture organism in 81.3% (65 of 80) of evaluable bloodstream infection episodes on the day of or after onset and in 51.9% (42 of 81) during the three days before; 82.7% (134 of 162) of control samples from patients without fever or infection had no bacterium or yeast detected. In 62 bronchoalveolar lavage specimens (Hu et al. 2026), a short-read MGI workflow and a host-depleted nanopore workflow both had 95.2% positive agreement with culture but 44.6% and 46.4% negative agreement, because they found organisms culture did not; against a composite reference that adds organisms found by both workflows, positive agreement was 93.3% and 90.7%. In 122 intensive-care patients with pneumonia-associated sepsis (Huang et al. 2026), a targeted probe-capture assay on plasma had 63.46% sensitivity against the reference diagnosis, against 35.58% for untargeted blood mNGS, 49.04% for conventional tests and 9.62% for blood culture, with specificity of 44.44% and 61.11% for the two blood sequencing assays. In mock communities (Portik et al. 2022), Kraken2 and Bracken called 44 to 204 absent species at a 0.001% read threshold (precision 0.05 to 0.21), while long-read MEGAN-LR and BugSeq-V2 called 0 to 2; the first author is a PacBio employee. In seven pathogen-free libraries scored against one shared virus database by the EsViritu developers (preprint), the median number of false virus species was 0 for EsViritu, Centrifuger and Sylph, 6 for Kraken2 and 18 for Metabuli. For M. tuberculosis reads in constructed metagenomes (Hall and Coin 2024), kraken with its standard database classified 0.07 to 0.74 of the M. tuberculosis reads as M. tuberculosis, against 0.97 to 0.995 with a Mycobacterium database. Two papers by the developers of trained classifiers compare them with the baseline tools, on simulated or isolate-derived data rather than clinical specimens. On simulated 1,500-nt genome fragments (Mock et al. 2022, BERTax), Kraken2 and minimap2 assigned a superkingdom to 76.11% and 75.59% of fragments, with 99.82% and 99.95% accuracy on the fragments they assigned, when relatives were in the reference, and to 21.56% and 19.88% with 90.71% and 94.42% accuracy when each fragment's genus was absent from it; BERTax assigned every fragment, with 94.78% and 88.95% accuracy in the two settings. On in silico mixtures of nanopore isolate reads from species absent from the reference (Peres da Silva et al. 2024, MetageNN), MetageNN assigned a genus to 93.26% of reads on average across 30 mixtures, against 64.90% for Kraken2 and 53.06% for MEGAN-LR (on minimap2 alignments); MMseqs2, a reference-based tool not in the baseline, assigned 85.49%. These shares count reads assigned, not reads assigned correctly. Each study used its own reference database and reporting rules, and none of these results is clinical validation.
source locator: amp-20261007-dna-pathogens-source: result amp-20261007-dna-pathogens-result; dna-pathogen-20261009-source-portik2022: Table 4; dna-pathogen-20261009-source-hall2024: Tables 5-8; dna-pathogen-20261011-wolf2026-source: Tables 2 and 3; dna-pathogen-20261011-hu2026-source: Table 2; dna-pathogen-20261011-huang2026-source: Table 2; rna-pathogen-20261011-tisza2026-source-supp: Supplemental Table S6; dna-pathogen-20261012-bertax-source: Materials and Methods 'Preparing Data for Fine-Tuning' (1,500-nt fragments; closely and distantly related selection); dna-pathogen-20261012-bertax-source-si: SI Table S2 (superkingdom acc. and prop.); dna-pathogen-20261012-metagenn-source: Results 'Read classification results' paragraph 1 and the pseudo-mock 'Experimental setup' paragraph
review: method: independent-cell-check; scope-review; method note: Matched every number in the text with the stored source_checked results on the reviewed evaluations of the use case's 25 active judgements, with a script written for this review. Read the five judgements added in PR #134 and the amended evidence gaps against the text. Checked that each cited source is source_checked with no evidence_concerns, that no withheld judgement is described, that nothing is recommended and that the text has no em or en dash.; reviewer: claude; reviewer note: Separate Claude review agent, independent of the agent that drafted the summary, of the agents that extracted the BERTax and MetageNN batches and of the 2026-10-12 reviewer; no human review claimed; reviewed at: 2026-10-14T13:30:00Z; note: Re-review requested in issue #145. The summary holds; no text, source or locator changes. Earlier review 2026-10-12 (docs/reviews/use-cases/dna-pathogen-summary-2026-10-12.md). Descriptive summary only; no execution, human scientific review or clinical validation. See docs/reviews/use-cases/dna-pathogen-summary-2026-10-14.md.
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