Configuration

Kraken2

Kraken 2 is the reference-database taxonomic classifier used in this metagenomic comparison.

Sources

Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 2. Materials and methods/2.3 Benchmarking performance (paragraph 4); 4. Discussion (paragraph 3)

1 evaluation · 1 metric row

How it worksEvaluated procedure (conceptual)

Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings.

Sources

Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 6); 2. Materials and methods/2.3 Benchmarking performance (paragraph 4)

At a glance

Model type

Reference-index taxonomic classifier; this record is the paper-specific evaluated configuration.

Sources

DerrickWood/kraken2 README.md · README.md model description

Biological inputs

Metagenomic reads or contigs and a taxonomic reference database

Sources

Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 1. Introduction (paragraph 6); 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 4)

Outputs

Taxonomic assignments

Sources

Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 1. Introduction (paragraph 6); 2. Materials and methods/2.3 Benchmarking performance (paragraph 2)

limited source coverage · Automated source review, 2026-09-16. All specifications and missing details

Evaluations and results

Release 2026-09-17-d277315f7d76 · 1 evaluation · 1 metric row. Different protocols are not a single leaderboard.

Evaluation setupMetricEvidence origin

Results grouped by the exact reported evaluation
Metric and finding	Coverage and uncertainty	Evidence
Kraken2: Simulated metagenome virus-taxon retrieval Configuration: Kraken2Task: Simulated metagenome virus-taxon retrievalDataset: Simulated viral metagenome Genus-rank viral taxon retrieval. Independent external evaluation · Evaluation metadata: needs review
0.627 Genus-level F1 Unit: unitless · Direction: unknown	Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported	source checkedNovel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · Table 1, Kraken2 / Genus row, F column Source checking is not independent reproduction.

How it works

How the evaluated method works

Sequence evidence is matched against a taxonomic reference index to assign reads or contigs. Database construction and the chosen confidence/settings remain part of the evaluated configuration.

Sources

Underlying method and version boundaries

Kraken 2 classifies sequences against a taxonomic reference index. The software version and the database used to construct that index are distinct reproducibility requirements.

Sources

DerrickWood/kraken2 README.md · README.md; introduction, model description, pretrained-model and usage sections at pinned revision

What was evaluated

The linked evaluation record identifies Kraken2: Simulated metagenome virus-taxon retrieval. Its dataset, split, adaptation and evidence origin remain attached to the reported results.

Sources

Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-b3-022

Strengths and limitations

Strengths and considerations

Provides an established reference-based comparator for learned or alignment-based taxonomic methods.
Sources
Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 4); 2. Materials and methods/2.3 Benchmarking performance (paragraph 1)

Limitations and conditions

Unrepresented organisms and reference contamination can alter assignments; results are specific to the database and query distribution.
Sources
Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 1. Introduction (paragraph 6); 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 7)

Profile review details

Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction.

Stable record: reported-model-673b8f46361000

Specifications

Inputs, training, access and other details

Explanatory profile: limited source coverage · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

Inputs, outputs and configuration
Property	Description and evidence
Model type	Reference-index taxonomic classifier; this record is the paper-specific evaluated configuration. Sources DerrickWood/kraken2 README.md · README.md model description
Architecture / procedure	Sequence evidence is matched against a taxonomic reference index to assign reads or contigs. Database construction and the chosen confidence/settings remain part of the evaluated configuration. Sources Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 6); 2. Materials and methods/2.3 Benchmarking performance (paragraph 4)
Biological inputs	Metagenomic reads or contigs and a taxonomic reference database Sources Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 1. Introduction (paragraph 6); 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 4)
Outputs	Taxonomic assignments Sources Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 1. Introduction (paragraph 6); 2. Materials and methods/2.3 Benchmarking performance (paragraph 2)
Parameters	Not applicable as a neural model size. · Not applicable Sources Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 4. Discussion (paragraph 2); Table veaa091-T5 (paragraph 1)
Known versions / configuration	Kraken2 is the comparison-table label; that label does not specify an immutable weight revision. · Not reported in inspected sources Sources Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label.
Training data / fitting	Reference-index construction rather than foundation-model pretraining. Sources Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 3. Results/3.1 Excellent recall and precision for both simulated and real datasets (paragraph 3); 3. Results/3.1 Excellent recall and precision for both simulated and real datasets (paragraph 4)
Context limits	Not applicable to a pretrained sequence-token window; read/contig lengths and the reference-database or comparison configuration determine the analysed input. · Not applicable Sources Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 1. Introduction (paragraph 6); 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 7)
Access	Official upstream implementation and usage documentation: https://github.com/DerrickWood/kraken2/blob/8c190b1b668825935dbf6dee5f969227dc8269bb/README.md. This pinned documentation revision is not automatically the evaluated weight revision. Sources DerrickWood/kraken2 README.md · README.md; installation, model download and usage instructions
Code licence	MIT (upstream repository code at the cited revision; this does not establish every dependency or historical checkpoint licence). Sources DerrickWood/kraken2 LICENSE · LICENSE; complete licence text
Weights licence	Not applicable: uses a reference index rather than a pretrained neural checkpoint. · Not applicable Sources Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 4. Discussion (paragraph 2); 2. Materials and methods/2.3 Benchmarking performance (paragraph 1)

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.

20 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-17-d277315f7d76
Property and statement	Original source and location	Review and provenance
Diagram caption Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings. Individual claims	Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types Original source ↗ 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 6); 2. Materials and methods/2.3 Benchmarking performance (paragraph 4) Version: version of record Retrieved: 2026-09-16T10:44:03.412605+00:00	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `77842d8e4f6b419e331ab5a01fdf8f9eb8604f259425d79602be896aad3d0ad1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram steps ["Metagenomic reads or contigs and a taxonomic reference database","Kraken2","Taxonomic assignments"] Individual claims	Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types Original source ↗ 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 6); 2. Materials and methods/2.3 Benchmarking performance (paragraph 4) Version: version of record Retrieved: 2026-09-16T10:44:03.412605+00:00	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `77842d8e4f6b419e331ab5a01fdf8f9eb8604f259425d79602be896aad3d0ad1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram title Evaluated procedure (conceptual) Individual claims	Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types Original source ↗ 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 6); 2. Materials and methods/2.3 Benchmarking performance (paragraph 4) Version: version of record Retrieved: 2026-09-16T10:44:03.412605+00:00	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `77842d8e4f6b419e331ab5a01fdf8f9eb8604f259425d79602be896aad3d0ad1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Model type Reference-index taxonomic classifier; this record is the paper-specific evaluated configuration. Individual claims	DerrickWood/kraken2 README.md Original source ↗ README.md model description Version: 8c190b1b668825935dbf6dee5f969227dc8269bb Retrieved: 2026-09-16T20:00:00.821204+00:00	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `2ea33af266b4268a55fd750d0f3265cd3165d61f6be375c5ea3b3ff5c58c7c8c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Architecture / procedure Sequence evidence is matched against a taxonomic reference index to assign reads or contigs. Database construction and the chosen confidence/settings remain part of the evaluated configuration. Individual claims	Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types Original source ↗ 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 6); 2. Materials and methods/2.3 Benchmarking performance (paragraph 4) Version: version of record Retrieved: 2026-09-16T10:44:03.412605+00:00	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `77842d8e4f6b419e331ab5a01fdf8f9eb8604f259425d79602be896aad3d0ad1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Weights licence Not applicable: uses a reference index rather than a pretrained neural checkpoint. Individual claims	Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types Original source ↗ 4. Discussion (paragraph 2); 2. Materials and methods/2.3 Benchmarking performance (paragraph 1) Version: version of record Retrieved: 2026-09-16T10:44:03.412605+00:00	inapplicable automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.10.value` Source artifact SHA-256: `77842d8e4f6b419e331ab5a01fdf8f9eb8604f259425d79602be896aad3d0ad1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Biological inputs Metagenomic reads or contigs and a taxonomic reference database Individual claims	Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types Original source ↗ 1. Introduction (paragraph 6); 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 4) Version: version of record Retrieved: 2026-09-16T10:44:03.412605+00:00	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.2.value` Source artifact SHA-256: `77842d8e4f6b419e331ab5a01fdf8f9eb8604f259425d79602be896aad3d0ad1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Outputs Taxonomic assignments Individual claims	Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types Original source ↗ 1. Introduction (paragraph 6); 2. Materials and methods/2.3 Benchmarking performance (paragraph 2) Version: version of record Retrieved: 2026-09-16T10:44:03.412605+00:00	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.3.value` Source artifact SHA-256: `77842d8e4f6b419e331ab5a01fdf8f9eb8604f259425d79602be896aad3d0ad1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Parameters Not applicable as a neural model size. Individual claims	Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types Original source ↗ 4. Discussion (paragraph 2); Table veaa091-T5 (paragraph 1) Version: version of record Retrieved: 2026-09-16T10:44:03.412605+00:00	inapplicable automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.4.value` Source artifact SHA-256: `77842d8e4f6b419e331ab5a01fdf8f9eb8604f259425d79602be896aad3d0ad1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Known versions / configuration Kraken2 is the comparison-table label; that label does not specify an immutable weight revision. Individual claims	Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types Original source ↗ Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. Version: version of record Retrieved: 2026-09-16T10:44:03.412605+00:00	unreported automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.5.value` Source artifact SHA-256: `77842d8e4f6b419e331ab5a01fdf8f9eb8604f259425d79602be896aad3d0ad1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

Release 2026-09-17-d277315f7d76 · Record review: needs review

3 source records and release history

Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · Original source · version of record
DerrickWood/kraken2 README.md · Original source · 8c190b1b668825935dbf6dee5f969227dc8269bb
DerrickWood/kraken2 LICENSE · Original source · 8c190b1b668825935dbf6dee5f969227dc8269bb

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Technical metadata and extraction receipts

Stable ID: reported-model-673b8f46361000

areas: microbes-communities
entity level: method
version: Not reported
reported name: Kraken2
historical missing metadata: version: not_reported_in_legacy_extract; checkpoint revision: not_reported_in_legacy_extract; training data: not_reported_in_legacy_extract; licence: not_reported_in_legacy_extract
metadata review scope: historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
legacy kinds: model
entity classification: review date: 2026-09-17; rationale: This source-scoped entry preserves the method/configuration actually named in an evaluation. It is neither a global family identity nor proof of an immutable checkpoint; the linked evaluation retains adaptation, fitting and scoring details.; source ids: lazypipe-2020; evidence-reported-base-kraken2-readme-md; source locator: 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 6); 2. Materials and methods/2.3 Benchmarking performance (paragraph 4) | README.md model description | 2. Materials and methods/2.3 Benchmarking performance (paragraph 4); 4. Discussion (paragraph 3); ambiguities: Configuration means the source-labelled evaluated identity. It does not establish missing checkpoint hashes, default settings or equivalence to same-named records in other papers.

Related records

model: Kraken2: Simulated metagenome virus-taxon retrieval

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