Method

Kraken2

Kraken 2 assigns taxonomic labels to sequence reads by consulting a reference-derived minimizer database.

Sources (4)

DerrickWood/kraken2: README.md; DerrickWood/kraken2: docs/MANUAL.markdown; DerrickWood/kraken2: docs/MANUAL.html; kraken2: Journal full-text XML · docs/MANUAL.markdown: Introduction, Standard Kraken 2 Database, Classification and Confidence scoring

0 evaluations · 0 metric rows

How it worksKraken2 workflow

Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation.

Sources (4)

At a glance

Model type

Minimizer-based taxonomic classifier

Sources (4)

Inputs

DNA reads or, in translated-search mode, sequences searched against an amino-acid database.

Sources (4)

Outputs

Per-read taxonomic assignments and aggregate classification reports.

Sources (4)

Source reviewed · Automated source review, 2026-09-16. All specifications and missing details

Evaluations and results

Release 2026-09-17-d277315f7d76 · 0 evaluations · 0 metric rows. Different protocols are not a single leaderboard.

No evaluations linked in this release.

How it works

Kraken 2 breaks query sequences into k-mers and looks up selected minimizers in a compact hash table. Each stored minimizer is associated with a lowest-common-ancestor taxonomic label. The classifier combines that evidence to assign a taxon; the reference database and confidence settings are therefore part of the evaluated procedure.

Sources (4)

Versions and reproducibility

Kraken 2 is a rewrite of Kraken 1 and is not backwards compatible. Read/contig input, not a learned fixed token window.

Sources (4)

Strengths and limitations

Strengths supported by sources

A reference-based procedural comparator with explicit database construction and confidence settings.
Sources (4)
DerrickWood/kraken2: README.md; DerrickWood/kraken2: docs/MANUAL.markdown; DerrickWood/kraken2: docs/MANUAL.html; kraken2: Journal full-text XML · docs/MANUAL.markdown: Introduction, Standard Kraken 2 Database, Classification and Confidence scoring

Limitations and conditions

Classification depends on the reference database, taxonomy version and minimizer configuration. Compact hashing can introduce false matches; software version alone does not identify a reproducible classifier.
Sources (4)
DerrickWood/kraken2: README.md; DerrickWood/kraken2: docs/MANUAL.markdown; DerrickWood/kraken2: docs/MANUAL.html; kraken2: Journal full-text XML · docs/MANUAL.markdown: Introduction, Standard Kraken 2 Database, Classification and Confidence scoring

Profile review details

Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied.

Stable record: catalog-model-kraken2

Specifications

Inputs, training, access and other details

Explanatory profile: source reviewed · 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	Minimizer-based taxonomic classifier Sources (4) DerrickWood/kraken2: README.md; DerrickWood/kraken2: docs/MANUAL.markdown; DerrickWood/kraken2: docs/MANUAL.html; kraken2: Journal full-text XML · docs/MANUAL.markdown: Introduction, Standard Kraken 2 Database, Classification and Confidence scoring
Architecture	Minimizer-based sequence classification using a compact hash table and lowest-common-ancestor taxonomy assignments. Sources (4) DerrickWood/kraken2: README.md; DerrickWood/kraken2: docs/MANUAL.markdown; DerrickWood/kraken2: docs/MANUAL.html; kraken2: Journal full-text XML · docs/MANUAL.markdown: Introduction, Standard Kraken 2 Database, Classification and Confidence scoring
Inputs	DNA reads or, in translated-search mode, sequences searched against an amino-acid database. Sources (4) DerrickWood/kraken2: README.md; DerrickWood/kraken2: docs/MANUAL.markdown; DerrickWood/kraken2: docs/MANUAL.html; kraken2: Journal full-text XML · docs/MANUAL.markdown: Introduction, Standard Kraken 2 Database, Classification and Confidence scoring
Outputs	Per-read taxonomic assignments and aggregate classification reports. Sources (4) DerrickWood/kraken2: README.md; DerrickWood/kraken2: docs/MANUAL.markdown; DerrickWood/kraken2: docs/MANUAL.html; kraken2: Journal full-text XML · docs/MANUAL.markdown: Introduction, Standard Kraken 2 Database, Classification and Confidence scoring
Parameters	Inapplicable as a neural parameter total; k-mer/minimizer length, confidence and database choices are algorithm settings. · Not applicable Sources (4) DerrickWood/kraken2: README.md; DerrickWood/kraken2: docs/MANUAL.markdown; DerrickWood/kraken2: docs/MANUAL.html; kraken2: Journal full-text XML · docs/MANUAL.markdown: Introduction, Standard Kraken 2 Database, Classification and Confidence scoring
Known versions	Kraken 2 is a rewrite of Kraken 1 and is not backwards compatible. Sources (4) DerrickWood/kraken2: README.md; DerrickWood/kraken2: docs/MANUAL.markdown; DerrickWood/kraken2: docs/MANUAL.html; kraken2: Journal full-text XML · docs/MANUAL.markdown: Introduction, Standard Kraken 2 Database, Classification and Confidence scoring
Training data	Not neural pretraining: build a database from selected reference sequences and taxonomy. Sources (4) DerrickWood/kraken2: README.md; DerrickWood/kraken2: docs/MANUAL.markdown; DerrickWood/kraken2: docs/MANUAL.html; kraken2: Journal full-text XML · docs/MANUAL.markdown: Introduction, Standard Kraken 2 Database, Classification and Confidence scoring
Training cutoff	Inapplicable to neural pretraining; reference-database and input-data dates must be recorded for each run. · Not applicable Sources (4) DerrickWood/kraken2: README.md; DerrickWood/kraken2: docs/MANUAL.markdown; DerrickWood/kraken2: docs/MANUAL.html; kraken2: Journal full-text XML · docs/MANUAL.markdown: Introduction, Standard Kraken 2 Database, Classification and Confidence scoring
Context limits	Read/contig input, not a learned fixed token window. Sources (4) DerrickWood/kraken2: README.md; DerrickWood/kraken2: docs/MANUAL.markdown; DerrickWood/kraken2: docs/MANUAL.html; kraken2: Journal full-text XML · docs/MANUAL.markdown: Introduction, Standard Kraken 2 Database, Classification and Confidence scoring
Weights licence	Inapplicable to this classifier: database contents and their licences replace neural weights. · Not applicable Sources (4) DerrickWood/kraken2: README.md; DerrickWood/kraken2: docs/MANUAL.markdown; DerrickWood/kraken2: docs/MANUAL.html; kraken2: Journal full-text XML · docs/MANUAL.markdown: Introduction, Standard Kraken 2 Database, Classification and Confidence scoring
Access	Official project documentation and implementation: https://github.com/DerrickWood/kraken2 Sources (4) DerrickWood/kraken2: README.md; DerrickWood/kraken2: docs/MANUAL.markdown; DerrickWood/kraken2: docs/MANUAL.html; kraken2: Journal full-text XML · docs/MANUAL.markdown: Introduction, Standard Kraken 2 Database, Classification and Confidence scoring
Code licence	MIT Sources DerrickWood/kraken2: LICENSE · LICENSE: licence text
Assumptions	Not extracted or verified for this record.

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.

77 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 summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims	kraken2: Journal full-text XML Original source ↗ docs/MANUAL.markdown: Introduction, Standard Kraken 2 Database, Classification and Confidence scoring Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009224+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `2fd1d7785b45855deacb566acc79336e292c4c2d4975095b2ff7b1200c406869` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims	DerrickWood/kraken2: docs/MANUAL.markdown Original source ↗ docs/MANUAL.markdown: Introduction, Standard Kraken 2 Database, Classification and Confidence scoring Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 8c190b1b668825935dbf6dee5f969227dc8269bb Retrieved: 2026-09-16T19:46:17.767980+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `182565cb02f3958b39b8303749e58cd8829c6c6bf4734e39533d86e7980071f7` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims	DerrickWood/kraken2: README.md Original source ↗ docs/MANUAL.markdown: Introduction, Standard Kraken 2 Database, Classification and Confidence scoring Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 8c190b1b668825935dbf6dee5f969227dc8269bb Retrieved: 2026-09-16T19:46:17.767980+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `2ea33af266b4268a55fd750d0f3265cd3165d61f6be375c5ea3b3ff5c58c7c8c` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims	DerrickWood/kraken2: docs/MANUAL.html Original source ↗ docs/MANUAL.markdown: Introduction, Standard Kraken 2 Database, Classification and Confidence scoring Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 8c190b1b668825935dbf6dee5f969227dc8269bb Retrieved: 2026-09-16T19:46:17.767980+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `ef0962a736771bfb8373905d612d64f334544d625236f89e54cf3a04c9737016` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps ["Reference genomes and taxonomy","Minimizer database","Read minimizer lookup","Taxonomic assignment"] Individual claims	kraken2: Journal full-text XML Original source ↗ docs/MANUAL.markdown: Introduction, Standard Kraken 2 Database, Classification and Confidence scoring Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009224+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `2fd1d7785b45855deacb566acc79336e292c4c2d4975095b2ff7b1200c406869` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps ["Reference genomes and taxonomy","Minimizer database","Read minimizer lookup","Taxonomic assignment"] Individual claims	DerrickWood/kraken2: docs/MANUAL.markdown Original source ↗ docs/MANUAL.markdown: Introduction, Standard Kraken 2 Database, Classification and Confidence scoring Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 8c190b1b668825935dbf6dee5f969227dc8269bb Retrieved: 2026-09-16T19:46:17.767980+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `182565cb02f3958b39b8303749e58cd8829c6c6bf4734e39533d86e7980071f7` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps ["Reference genomes and taxonomy","Minimizer database","Read minimizer lookup","Taxonomic assignment"] Individual claims	DerrickWood/kraken2: README.md Original source ↗ docs/MANUAL.markdown: Introduction, Standard Kraken 2 Database, Classification and Confidence scoring Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 8c190b1b668825935dbf6dee5f969227dc8269bb Retrieved: 2026-09-16T19:46:17.767980+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `2ea33af266b4268a55fd750d0f3265cd3165d61f6be375c5ea3b3ff5c58c7c8c` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps ["Reference genomes and taxonomy","Minimizer database","Read minimizer lookup","Taxonomic assignment"] Individual claims	DerrickWood/kraken2: docs/MANUAL.html Original source ↗ docs/MANUAL.markdown: Introduction, Standard Kraken 2 Database, Classification and Confidence scoring Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 8c190b1b668825935dbf6dee5f969227dc8269bb Retrieved: 2026-09-16T19:46:17.767980+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `ef0962a736771bfb8373905d612d64f334544d625236f89e54cf3a04c9737016` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title Kraken2 workflow Individual claims	kraken2: Journal full-text XML Original source ↗ docs/MANUAL.markdown: Introduction, Standard Kraken 2 Database, Classification and Confidence scoring Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009224+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `2fd1d7785b45855deacb566acc79336e292c4c2d4975095b2ff7b1200c406869` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title Kraken2 workflow Individual claims	DerrickWood/kraken2: docs/MANUAL.markdown Original source ↗ docs/MANUAL.markdown: Introduction, Standard Kraken 2 Database, Classification and Confidence scoring Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 8c190b1b668825935dbf6dee5f969227dc8269bb Retrieved: 2026-09-16T19:46:17.767980+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `182565cb02f3958b39b8303749e58cd8829c6c6bf4734e39533d86e7980071f7` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact

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Sources and history

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

6 source records and release history

Kraken2 official resource · Original source · Not reported
DerrickWood/kraken2: README.md · Original source · 8c190b1b668825935dbf6dee5f969227dc8269bb
DerrickWood/kraken2: docs/MANUAL.markdown · Original source · 8c190b1b668825935dbf6dee5f969227dc8269bb
DerrickWood/kraken2: docs/MANUAL.html · Original source · 8c190b1b668825935dbf6dee5f969227dc8269bb
kraken2: Journal full-text XML · Original source · Retrieved page snapshot; no immutable publisher revision supplied
DerrickWood/kraken2: LICENSE · Original source · 8c190b1b668825935dbf6dee5f969227dc8269bb

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Technical metadata and extraction receipts

Stable ID: catalog-model-kraken2

areas: microbes-communities
method types: baseline
entity level: family
version: current database pinned at run time
reported name: Kraken2
access: Public classifier; database build/version must be pinned separately.
method type: baseline
historical missing metadata: checkpoint revision: not_yet_extracted; training data: not_yet_extracted; licence: not_yet_extracted
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: The cited architecture/procedure describes an algorithm, representation recipe or software toolkit, rather than a single released learned biological model. Fitted models, selected reference databases and concrete runs remain separate configurations.; source ids: evidence-official-40f46dc4b9fcc306773b; evidence-official-33fe0374c8ebbc2c7294; evidence-official-9ba2b6dc494c7b6df951; evidence-official-1f756fefa823dd402b0f; source locator: docs/MANUAL.markdown: Introduction, Standard Kraken 2 Database, Classification and Confidence scoring; ambiguities: None recorded

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model: Kraken2

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