Configuration

GTDB-Tk

GTDB-Tk classifies metagenome-assembled genomes in the kMetaShot comparison.

Sources

kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes · Materials and methods/GTDBtk taxonomy conversion (paragraph 1); Results (paragraph 1)

1 evaluation · 1 result

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

kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes · Materials and methods/GTDBtk taxonomy conversion (paragraph 1); Materials and methods (paragraph 1)

Overview

Model type

Genome-taxonomy toolkit; this record is the paper-specific evaluated configuration.

Sources

Ecogenomics/GTDBTk README.md · README.md model description

Biological inputs

Bacterial or archaeal genome assemblies/MAGs

Sources

kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes · Results (paragraph 1); Materials and methods (paragraph 1)

Outputs

GTDB taxonomic assignments

Sources

kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes · Materials and methods/Taxonomic classification algorithm (paragraph 5); Materials and methods/GTDBtk taxonomy conversion (paragraph 1)

Access

Official upstream implementation and usage documentation: https://github.com/Ecogenomics/GTDBTk/blob/f17decef1f9d9cf5b4d31fd21f5c9d32d813abdc/README.md. This pinned documentation revision is not automatically the evaluated weight revision.

Sources

Ecogenomics/GTDBTk README.md · README.md; installation, model download and usage instructions

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

Evaluations and results

1 evaluation · 1 result. Different protocols are not a single leaderboard.

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: GTDB-Tk	Task: Mock-community MAG taxonomy classification Dataset: Real mock community MAGs	89.8 Genus-level F1 % · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GTDB-Tk: Mock-community MAG taxonomy classification Genus classification of the same MAG set. Aggregation: Not reported kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes · Table 2, F1-score % row, Genus Gtk column

Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.

Use this model

How it works, versions and access

How it works

How the evaluated method works

Marker identification and sequence alignment place genomes in the Genome Taxonomy Database framework.

Sources

kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes · Materials and methods/GTDBtk taxonomy conversion (paragraph 1); Materials and methods (paragraph 1)

Underlying method and version boundaries

GTDB-Tk assigns bacterial and archaeal genomes to the Genome Taxonomy Database and supports MAGs, isolate genomes and single-cell genomes. Historical GTDB-Tk versions and GTDB data releases must be retained together.

Sources

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

What was evaluated

The linked evaluation record identifies GTDB-Tk: Mock-community MAG taxonomy classification. Its dataset, split, adaptation and evidence origin remain attached to the reported results.

Sources

kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-b3-030

Strengths, limitations and unresolved questions

Strengths and limitations

Strengths and considerations

Uses a genome- and phylogeny-based reference procedure.
Sources
kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes · Materials and methods/kMetaShot reference module (paragraph 10); Materials and methods/kMetaShot reference module (paragraph 6)

Limitations and conditions

Database release and genome completeness affect classification; this record is an older evaluated version, not the current software release.
Sources
kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes · Materials and methods/kMetaShot testing on Human Microbiome Project genomes (paragraph 1); Materials and methods/GTDBtk taxonomy conversion (paragraph 1)

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-3fd1e9f6c573b2

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	Genome-taxonomy toolkit; this record is the paper-specific evaluated configuration. Sources Ecogenomics/GTDBTk README.md · README.md model description
Architecture / procedure	Marker identification and sequence alignment place genomes in the Genome Taxonomy Database framework. Sources kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes · Materials and methods/GTDBtk taxonomy conversion (paragraph 1); Materials and methods (paragraph 1)
Biological inputs	Bacterial or archaeal genome assemblies/MAGs Sources kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes · Results (paragraph 1); Materials and methods (paragraph 1)
Outputs	GTDB taxonomic assignments Sources kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes · Materials and methods/Taxonomic classification algorithm (paragraph 5); Materials and methods/GTDBtk taxonomy conversion (paragraph 1)
Parameters	Not applicable: this is a reference-database algorithm rather than a neural model. · Not applicable Sources kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes · Materials and methods/kMetaShot reference module (paragraph 9); Materials and methods/kMetaShot reference module (paragraph 10)
Known versions / configuration	GTDB-Tk v1.0.2 in the reported CAMI II comparison · Not reported in inspected sources Sources kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes · Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label.
Training data / fitting	Reference taxonomy and genome database rather than a pretrained neural model. Sources kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes · Materials and methods/GTDBtk taxonomy conversion (paragraph 1); Results/Benchmarking on the in silico Critical Assessment of Metagenome Interpretation II datasets (paragraph 1)
Context limits	Not applicable to a learned context window; the analysed reads/genomes and versioned reference database define the workload. · Not applicable Sources kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes · Results (paragraph 1); Materials and methods (paragraph 1)
Access	Official upstream implementation and usage documentation: https://github.com/Ecogenomics/GTDBTk/blob/f17decef1f9d9cf5b4d31fd21f5c9d32d813abdc/README.md. This pinned documentation revision is not automatically the evaluated weight revision. Sources Ecogenomics/GTDBTk README.md · README.md; installation, model download and usage instructions
Code licence	GNU GPL version 3 (upstream repository code at the cited revision; this does not establish every dependency or historical checkpoint licence). Sources Ecogenomics/GTDBTk LICENSE · LICENSE; complete licence text
Weights licence	Not applicable to neural weights; reference-database access and reuse terms are separate. · Not applicable Sources kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes · Materials and methods/kMetaShot reference module (paragraph 10); Materials and methods/Evaluation of computational requirements (paragraph 1)

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.

20 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
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	kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes Original source ↗ Materials and methods/GTDBtk taxonomy conversion (paragraph 1); Materials and methods (paragraph 1) Version: PMC archival version PMC11695915.1 Retrieved: 2026-09-16T10:44:03.417367+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: `4584e93ea035c1170b8756a0a52cbe99fe72e70bd09b5f1dee639ee104f78247` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram steps Bacterial or archaeal genome assemblies/MAGs GTDB-Tk GTDB taxonomic assignments Individual claims	kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes Original source ↗ Materials and methods/GTDBtk taxonomy conversion (paragraph 1); Materials and methods (paragraph 1) Version: PMC archival version PMC11695915.1 Retrieved: 2026-09-16T10:44:03.417367+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: `4584e93ea035c1170b8756a0a52cbe99fe72e70bd09b5f1dee639ee104f78247` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram title Evaluated procedure (conceptual) Individual claims	kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes Original source ↗ Materials and methods/GTDBtk taxonomy conversion (paragraph 1); Materials and methods (paragraph 1) Version: PMC archival version PMC11695915.1 Retrieved: 2026-09-16T10:44:03.417367+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: `4584e93ea035c1170b8756a0a52cbe99fe72e70bd09b5f1dee639ee104f78247` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Model type Genome-taxonomy toolkit; this record is the paper-specific evaluated configuration. Individual claims	Ecogenomics/GTDBTk README.md Original source ↗ README.md model description Version: f17decef1f9d9cf5b4d31fd21f5c9d32d813abdc Retrieved: 2026-09-16T20:00:03.977720+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: `72124a5fb40dc02379ca775daae2bf894bc9e1b240a0a31d65e6c6c5c99e268c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Architecture / procedure Marker identification and sequence alignment place genomes in the Genome Taxonomy Database framework. Individual claims	kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes Original source ↗ Materials and methods/GTDBtk taxonomy conversion (paragraph 1); Materials and methods (paragraph 1) Version: PMC archival version PMC11695915.1 Retrieved: 2026-09-16T10:44:03.417367+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: `4584e93ea035c1170b8756a0a52cbe99fe72e70bd09b5f1dee639ee104f78247` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Weights licence Not applicable to neural weights; reference-database access and reuse terms are separate. Individual claims	kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes Original source ↗ Materials and methods/kMetaShot reference module (paragraph 10); Materials and methods/Evaluation of computational requirements (paragraph 1) Version: PMC archival version PMC11695915.1 Retrieved: 2026-09-16T10:44:03.417367+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: `4584e93ea035c1170b8756a0a52cbe99fe72e70bd09b5f1dee639ee104f78247` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Biological inputs Bacterial or archaeal genome assemblies/MAGs Individual claims	kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes Original source ↗ Results (paragraph 1); Materials and methods (paragraph 1) Version: PMC archival version PMC11695915.1 Retrieved: 2026-09-16T10:44:03.417367+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: `4584e93ea035c1170b8756a0a52cbe99fe72e70bd09b5f1dee639ee104f78247` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Outputs GTDB taxonomic assignments Individual claims	kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes Original source ↗ Materials and methods/Taxonomic classification algorithm (paragraph 5); Materials and methods/GTDBtk taxonomy conversion (paragraph 1) Version: PMC archival version PMC11695915.1 Retrieved: 2026-09-16T10:44:03.417367+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: `4584e93ea035c1170b8756a0a52cbe99fe72e70bd09b5f1dee639ee104f78247` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Parameters Not applicable: this is a reference-database algorithm rather than a neural model. Individual claims	kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes Original source ↗ Materials and methods/kMetaShot reference module (paragraph 9); Materials and methods/kMetaShot reference module (paragraph 10) Version: PMC archival version PMC11695915.1 Retrieved: 2026-09-16T10:44:03.417367+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: `4584e93ea035c1170b8756a0a52cbe99fe72e70bd09b5f1dee639ee104f78247` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Known versions / configuration GTDB-Tk v1.0.2 in the reported CAMI II comparison Individual claims	kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes Original source ↗ Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. Version: PMC archival version PMC11695915.1 Retrieved: 2026-09-16T10:44:03.417367+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: `4584e93ea035c1170b8756a0a52cbe99fe72e70bd09b5f1dee639ee104f78247` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

View linked audit checks and correction history

Release 2026-09-29-06401fd5b220 · Record review: needs review

3 source records and release history

kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes · Original source · PMC archival version PMC11695915.1
Ecogenomics/GTDBTk README.md · Original source · f17decef1f9d9cf5b4d31fd21f5c9d32d813abdc
Ecogenomics/GTDBTk LICENSE · Original source · f17decef1f9d9cf5b4d31fd21f5c9d32d813abdc

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Technical metadata and extraction receipts

Stable ID: reported-model-3fd1e9f6c573b2

areas: microbes-communities
entity level: method
version: Not reported
reported name: GTDB-Tk
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: kmetashot-2025; evidence-reported-base-gtdbtk-readme-md; source locator: Materials and methods/GTDBtk taxonomy conversion (paragraph 1); Materials and methods (paragraph 1) | README.md model description | Materials and methods/GTDBtk taxonomy conversion (paragraph 1); Results (paragraph 1); 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: GTDB-Tk: Mock-community MAG taxonomy classification

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