Evidence claim

Kraken: description

Evidence concern: excluded from comparisons

Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing'

Description of Kraken

Classifier that assigns taxonomic labels to metagenomic DNA sequences by exact alignment of k-mers.

Replace a placeholder or provenance description with a sourced functional description (issue #88 follow-up). Historical releases retain the original value.

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.

14 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Claimed field description Context-only references	Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection Original source ↗ qa-descriptions-20261011-source-kraken: abstractText; dna-pathogen-20261009-source-song2025: Methods 'Data Analysis' paragraph 1 (cites Wood and Salzberg 2014) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: MicrobiologyOpen 14(6):e70158, published online 2025-12-15; PMC12705909 full-text XML Retrieved: 2026-10-09T19:48:48Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.field` Source artifact SHA-256: `7b122b551b2155b43c26f5a15e7382a0662d859520d2939dc91e04d88e5656ef` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field description Context-only references	Abstract: Kraken: ultrafast metagenomic sequence classification using exact alignments Original source ↗ qa-descriptions-20261011-source-kraken: abstractText; dna-pathogen-20261009-source-song2025: Methods 'Data Analysis' paragraph 1 (cites Wood and Salzberg 2014) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Europe PMC core record MED/24580807 (title and abstract), Genome biology 2014 Retrieved: 2026-10-11T00:29:23Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `5209b274d6ff9f32c554eced5ccb1cd810194fe587a7649b4ca5990e870fd07d` Hash scope: SHA-256 of one retrieval of a Europe PMC REST search response. These responses are not byte-stable (a later retrieval can differ in JSON key order); the title and abstractText fields are the evidence. Inspected artifact
Previous value Exact k-mer classifier with lowest common ancestor assignment, cited as Wood and Salzberg 2014. Context-only references	Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection Original source ↗ qa-descriptions-20261011-source-kraken: abstractText; dna-pathogen-20261009-source-song2025: Methods 'Data Analysis' paragraph 1 (cites Wood and Salzberg 2014) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: MicrobiologyOpen 14(6):e70158, published online 2025-12-15; PMC12705909 full-text XML Retrieved: 2026-10-09T19:48:48Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.previous_value` Source artifact SHA-256: `7b122b551b2155b43c26f5a15e7382a0662d859520d2939dc91e04d88e5656ef` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Previous value Exact k-mer classifier with lowest common ancestor assignment, cited as Wood and Salzberg 2014. Context-only references	Abstract: Kraken: ultrafast metagenomic sequence classification using exact alignments Original source ↗ qa-descriptions-20261011-source-kraken: abstractText; dna-pathogen-20261009-source-song2025: Methods 'Data Analysis' paragraph 1 (cites Wood and Salzberg 2014) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Europe PMC core record MED/24580807 (title and abstract), Genome biology 2014 Retrieved: 2026-10-11T00:29:23Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.previous_value` Source artifact SHA-256: `5209b274d6ff9f32c554eced5ccb1cd810194fe587a7649b4ca5990e870fd07d` Hash scope: SHA-256 of one retrieval of a Europe PMC REST search response. These responses are not byte-stable (a later retrieval can differ in JSON key order); the title and abstractText fields are the evidence. Inspected artifact
Source location qa-descriptions-20261011-source-kraken: abstractText; dna-pathogen-20261009-source-song2025: Methods 'Data Analysis' paragraph 1 (cites Wood and Salzberg 2014) Context-only references	Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection Original source ↗ qa-descriptions-20261011-source-kraken: abstractText; dna-pathogen-20261009-source-song2025: Methods 'Data Analysis' paragraph 1 (cites Wood and Salzberg 2014) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: MicrobiologyOpen 14(6):e70158, published online 2025-12-15; PMC12705909 full-text XML Retrieved: 2026-10-09T19:48:48Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.source_locator` Source artifact SHA-256: `7b122b551b2155b43c26f5a15e7382a0662d859520d2939dc91e04d88e5656ef` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location qa-descriptions-20261011-source-kraken: abstractText; dna-pathogen-20261009-source-song2025: Methods 'Data Analysis' paragraph 1 (cites Wood and Salzberg 2014) Context-only references	Abstract: Kraken: ultrafast metagenomic sequence classification using exact alignments Original source ↗ qa-descriptions-20261011-source-kraken: abstractText; dna-pathogen-20261009-source-song2025: Methods 'Data Analysis' paragraph 1 (cites Wood and Salzberg 2014) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Europe PMC core record MED/24580807 (title and abstract), Genome biology 2014 Retrieved: 2026-10-11T00:29:23Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `5209b274d6ff9f32c554eced5ccb1cd810194fe587a7649b4ca5990e870fd07d` Hash scope: SHA-256 of one retrieval of a Europe PMC REST search response. These responses are not byte-stable (a later retrieval can differ in JSON key order); the title and abstractText fields are the evidence. Inspected artifact
Claimed value Classifier that assigns taxonomic labels to metagenomic DNA sequences by exact alignment of k-mers. Context-only references	Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection Original source ↗ qa-descriptions-20261011-source-kraken: abstractText; dna-pathogen-20261009-source-song2025: Methods 'Data Analysis' paragraph 1 (cites Wood and Salzberg 2014) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: MicrobiologyOpen 14(6):e70158, published online 2025-12-15; PMC12705909 full-text XML Retrieved: 2026-10-09T19:48:48Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.value` Source artifact SHA-256: `7b122b551b2155b43c26f5a15e7382a0662d859520d2939dc91e04d88e5656ef` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed value Classifier that assigns taxonomic labels to metagenomic DNA sequences by exact alignment of k-mers. Context-only references	Abstract: Kraken: ultrafast metagenomic sequence classification using exact alignments Original source ↗ qa-descriptions-20261011-source-kraken: abstractText; dna-pathogen-20261009-source-song2025: Methods 'Data Analysis' paragraph 1 (cites Wood and Salzberg 2014) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Europe PMC core record MED/24580807 (title and abstract), Genome biology 2014 Retrieved: 2026-10-11T00:29:23Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.value` Source artifact SHA-256: `5209b274d6ff9f32c554eced5ccb1cd810194fe587a7649b4ca5990e870fd07d` Hash scope: SHA-256 of one retrieval of a Europe PMC REST search response. These responses are not byte-stable (a later retrieval can differ in JSON key order); the title and abstractText fields are the evidence. Inspected artifact
Description Replace a placeholder or provenance description with a sourced functional description (issue #88 follow-up). Historical releases retain the original value. Context-only references	Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection Original source ↗ qa-descriptions-20261011-source-kraken: abstractText; dna-pathogen-20261009-source-song2025: Methods 'Data Analysis' paragraph 1 (cites Wood and Salzberg 2014) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: MicrobiologyOpen 14(6):e70158, published online 2025-12-15; PMC12705909 full-text XML Retrieved: 2026-10-09T19:48:48Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `description` Source artifact SHA-256: `7b122b551b2155b43c26f5a15e7382a0662d859520d2939dc91e04d88e5656ef` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description Replace a placeholder or provenance description with a sourced functional description (issue #88 follow-up). Historical releases retain the original value. Context-only references	Abstract: Kraken: ultrafast metagenomic sequence classification using exact alignments Original source ↗ qa-descriptions-20261011-source-kraken: abstractText; dna-pathogen-20261009-source-song2025: Methods 'Data Analysis' paragraph 1 (cites Wood and Salzberg 2014) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Europe PMC core record MED/24580807 (title and abstract), Genome biology 2014 Retrieved: 2026-10-11T00:29:23Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `5209b274d6ff9f32c554eced5ccb1cd810194fe587a7649b4ca5990e870fd07d` Hash scope: SHA-256 of one retrieval of a Europe PMC REST search response. These responses are not byte-stable (a later retrieval can differ in JSON key order); the title and abstractText fields are the evidence. Inspected artifact

How to read the evidence

Sources and history

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

2 source records and release history

Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Original source · MicrobiologyOpen 14(6):e70158, published online 2025-12-15; PMC12705909 full-text XML
Abstract: Kraken: ultrafast metagenomic sequence classification using exact alignments · Original source · Europe PMC core record MED/24580807 (title and abstract), Genome biology 2014

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Technical metadata and extraction receipts

Stable ID: metadata-correction-6ea29bf7a1fb96a2bf63

areas: microbes-communities
contexts: clinical_research
method types: conventional_pipeline
field: description
previous value: Exact k-mer classifier with lowest common ancestor assignment, cited as Wood and Salzberg 2014.
value: Classifier that assigns taxonomic labels to metagenomic DNA sequences by exact alignment of k-mers.
source locator: qa-descriptions-20261011-source-kraken: abstractText; dna-pathogen-20261009-source-song2025: Methods 'Data Analysis' paragraph 1 (cites Wood and Salzberg 2014)
review: method: automated-source-review; ai-assisted-source-review; reviewer: claude; reviewer note: Extractor: Claude research agent for the issue #88 follow-up. Reviewer: separate Claude review agent, independent of the extractor; no human review claimed; date: 2026-10-11; method note: Re-downloaded the cited artifact and checked its SHA-256 against the pin, read the new description against the cited passage, compared previous_value with origin/main, and ran build.py --check.; note: Replace a placeholder or provenance description with a sourced functional description (issue #88 follow-up). Historical releases retain the original value. Independent review 2026-10-11: Supported by the Kraken abstractText ('assigning taxonomic labels to metagenomic DNA sequences'; 'Using exact alignment of k-mers'). Agree with dropping 'lowest common ancestor assignment': it is not in the pinned abstract. The citation formerly in the text is now the added source.

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subject: Kraken

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