Model type
Reference-index taxonomic classifier; this record is the paper-specific evaluated configuration.
Configuration
Kraken 2
Kraken 2 is the reference-database taxonomic classifier used in this metagenomic comparison.
Sources
Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Discussion (paragraph 4); Methods/Method Comparison (paragraph 1)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
Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Methods/Competitive read alignment with Magnet (paragraph 1); Results/Method overview (paragraph 1)At a glance
Biological inputs
Metagenomic reads or contigs and a taxonomic reference database
Sources
Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Discussion (paragraph 4); Methods/Lemur (paragraph 8)Outputs
Taxonomic assignments
Sources
Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Methods/Lemur (paragraph 2); Methods/Lemur (paragraph 8)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.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| Kraken 2: Long-read taxonomic profiling Mean across five replicate runs on Zymo LOG 10%. Independent external evaluation · Evaluation metadata: needs review | ||
| 0.375 F1 Unit: unitless · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedLightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Table 3, LOG 10% / Kraken 2 row, F1 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
Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Methods/Competitive read alignment with Magnet (paragraph 1); Results/Method overview (paragraph 1)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 revisionWhat was evaluated
The linked evaluation record identifies Kraken 2: Long-read taxonomic profiling. Its dataset, split, adaptation and evidence origin remain attached to the reported results.
Sources
Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-b3-032Strengths and limitations
Strengths and considerations
- Provides an established reference-based comparator for learned or alignment-based taxonomic methods.
Sources
Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Methods/Lemur (paragraph 8); Methods/Competitive read alignment with Magnet (paragraph 1)
Limitations and conditions
- Unrepresented organisms and reference contamination can alter assignments; results are specific to the database and query distribution.
Sources
Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Discussion (paragraph 4); Results/Prior simulated data (paragraph 2)
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-62bc5e5ba13e7dSpecifications
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.
| Property | Description and evidence |
|---|---|
| Model type | Reference-index taxonomic classifier; this record is the paper-specific evaluated configuration.SourcesDerrickWood/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.SourcesLightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Methods/Competitive read alignment with Magnet (paragraph 1); Results/Method overview (paragraph 1) |
| Biological inputs | Metagenomic reads or contigs and a taxonomic reference databaseSourcesLightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Discussion (paragraph 4); Methods/Lemur (paragraph 8) |
| Outputs | Taxonomic assignmentsSourcesLightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Methods/Lemur (paragraph 2); Methods/Lemur (paragraph 8) |
| Parameters | Not applicable as a neural model size. · Not applicableSourcesLightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Methods/Synthetic and simulated datasets/Simulated data from (Dilthey et al. 2019) (paragraph 1); Methods/Synthetic and simulated datasets/Zymo Fecal Reference with TruMatrix (paragraph 1) |
| Known versions / configuration | Kraken 2 is the comparison-table label; that label does not specify an immutable weight revision. · Not reported in inspected sourcesSourcesLightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · 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.SourcesLightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Methods/Synthetic and simulated datasets/Zymo Fecal Reference with TruMatrix (paragraph 1); Methods/Synthetic and simulated datasets/Zymo Fecal Reference with TruMatrix (paragraph 2) |
| 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 applicableSourcesLightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Methods/Competitive read alignment with Magnet (paragraph 1); Discussion (paragraph 2) |
| 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.SourcesDerrickWood/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).SourcesDerrickWood/kraken2 LICENSE · LICENSE; complete licence text |
| Weights licence | Not applicable: uses a reference index rather than a pretrained neural checkpoint. · Not applicableSourcesLightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Methods/Competitive read alignment with Magnet (paragraph 1); Results/ZymoBIOMICS Fecal Reference (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
| 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 | Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet Methods/Competitive read alignment with Magnet (paragraph 1); Results/Method overview (paragraph 1) Version: PMC archival version PMC11185576.2 | source checked automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram steps ["Metagenomic reads or contigs and a taxonomic reference database","Kraken 2","Taxonomic assignments"] Individual claims | Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet Methods/Competitive read alignment with Magnet (paragraph 1); Results/Method overview (paragraph 1) Version: PMC archival version PMC11185576.2 | source checked automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Evaluated procedure (conceptual) Individual claims | Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet Methods/Competitive read alignment with Magnet (paragraph 1); Results/Method overview (paragraph 1) Version: PMC archival version PMC11185576.2 | source checked automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Model type Reference-index taxonomic classifier; this record is the paper-specific evaluated configuration. Individual claims | DerrickWood/kraken2 README.md README.md model description Version: 8c190b1b668825935dbf6dee5f969227dc8269bb | source checked automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| 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 | Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet Methods/Competitive read alignment with Magnet (paragraph 1); Results/Method overview (paragraph 1) Version: PMC archival version PMC11185576.2 | source checked automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Weights licence Not applicable: uses a reference index rather than a pretrained neural checkpoint. Individual claims | Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet Methods/Competitive read alignment with Magnet (paragraph 1); Results/ZymoBIOMICS Fecal Reference (paragraph 1) Version: PMC archival version PMC11185576.2 | inapplicable automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Biological inputs Metagenomic reads or contigs and a taxonomic reference database Individual claims | Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet Discussion (paragraph 4); Methods/Lemur (paragraph 8) Version: PMC archival version PMC11185576.2 | source checked automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Outputs Taxonomic assignments Individual claims | Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet Methods/Lemur (paragraph 2); Methods/Lemur (paragraph 8) Version: PMC archival version PMC11185576.2 | source checked automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Parameters Not applicable as a neural model size. Individual claims | Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet Methods/Synthetic and simulated datasets/Simulated data from (Dilthey et al. 2019) (paragraph 1); Methods/Synthetic and simulated datasets/Zymo Fecal Reference with TruMatrix (paragraph 1) Version: PMC archival version PMC11185576.2 | inapplicable automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Known versions / configuration Kraken 2 is the comparison-table label; that label does not specify an immutable weight revision. Individual claims | Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. Version: PMC archival version PMC11185576.2 | unreported automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: needs review
3 source records and release history
- Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Original source · PMC archival version PMC11185576.2
- DerrickWood/kraken2 README.md · Original source · 8c190b1b668825935dbf6dee5f969227dc8269bb
- DerrickWood/kraken2 LICENSE · Original source · 8c190b1b668825935dbf6dee5f969227dc8269bb
Technical metadata and extraction receipts
Stable ID: reported-model-62bc5e5ba13e7d
- areas
- microbes-communities
- entity level
- method
- version
- Not reported
- reported name
- Kraken 2
- 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: lemur-magnet-2024; evidence-reported-base-kraken2-readme-md; source locator: Methods/Competitive read alignment with Magnet (paragraph 1); Results/Method overview (paragraph 1) | README.md model description | Discussion (paragraph 4); Methods/Method Comparison (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.