Model type
Reference-index taxonomic classifier; this record is the paper-specific evaluated configuration.
Configuration
Kraken2
Kraken 2 is the reference-database taxonomic classifier used in this metagenomic comparison.
Sources
Strain level microbial detection and quantification with applications to single cell metagenomics · Introduction (paragraph 3); Introduction (paragraph 4)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
Strain level microbial detection and quantification with applications to single cell metagenomics · Methods (paragraph 7); Methods (paragraph 1)At a glance
Biological inputs
Metagenomic reads or contigs and a taxonomic reference database
Sources
Strain level microbial detection and quantification with applications to single cell metagenomics · Introduction (paragraph 4); Results/Precision and recall in read classification across all species level queries (paragraph 3)Outputs
Taxonomic assignments
Sources
Strain level microbial detection and quantification with applications to single cell metagenomics · Results/Performance of CAMMiQ on real single-cell metatranscriptomic queries (paragraph 5); Introduction (paragraph 4)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 |
|---|---|---|
| Kraken2: Strain-level abundance quantification Configuration: Kraken2Task: Strain-level abundance quantificationDataset: HumanGut-all strain-level query Strain-level quantification on the HumanGut-all synthetic query. Independent external evaluation · Evaluation metadata: needs review | ||
| 0.2841 L1 abundance error Unit: unitless · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedStrain level microbial detection and quantification with applications to single cell metagenomics · Table 5, B. L1 Err. / HumanGut-all row, Kraken2 L1 Err. 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
Strain level microbial detection and quantification with applications to single cell metagenomics · Methods (paragraph 7); Methods (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 Kraken2: Strain-level abundance quantification. Its dataset, split, adaptation and evidence origin remain attached to the reported results.
Sources
Strain level microbial detection and quantification with applications to single cell metagenomics · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-b3-020Strengths and limitations
Strengths and considerations
- Provides an established reference-based comparator for learned or alignment-based taxonomic methods.
Sources
Strain level microbial detection and quantification with applications to single cell metagenomics · Introduction (paragraph 2); Introduction (paragraph 4)
Limitations and conditions
- Unrepresented organisms and reference contamination can alter assignments; results are specific to the database and query distribution.
Sources
Strain level microbial detection and quantification with applications to single cell metagenomics · Introduction (paragraph 4); Introduction (paragraph 3)
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-70f57ebb163a5cSpecifications
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.SourcesStrain level microbial detection and quantification with applications to single cell metagenomics · Methods (paragraph 7); Methods (paragraph 1) |
| Biological inputs | Metagenomic reads or contigs and a taxonomic reference databaseSourcesStrain level microbial detection and quantification with applications to single cell metagenomics · Introduction (paragraph 4); Results/Precision and recall in read classification across all species level queries (paragraph 3) |
| Outputs | Taxonomic assignmentsSourcesStrain level microbial detection and quantification with applications to single cell metagenomics · Results/Performance of CAMMiQ on real single-cell metatranscriptomic queries (paragraph 5); Introduction (paragraph 4) |
| Parameters | Not applicable as a neural model size. · Not applicableSourcesStrain level microbial detection and quantification with applications to single cell metagenomics · Methods/CAMMiQ Index/Sparsifying unique substrings (paragraph 1); Methods/Query processing stage 2: ILP formulation (paragraph 4) |
| Known versions / configuration | Kraken2 is the comparison-table label; that label does not specify an immutable weight revision. · Not reported in inspected sourcesSourcesStrain level microbial detection and quantification with applications to single cell metagenomics · 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.SourcesStrain level microbial detection and quantification with applications to single cell metagenomics · Results/Datasets (paragraph 1); Results/Datasets (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 applicableSourcesStrain level microbial detection and quantification with applications to single cell metagenomics · Methods (paragraph 1); Introduction (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.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 applicableSourcesStrain level microbial detection and quantification with applications to single cell metagenomics · Results/Precision and recall in read classification across all species level queries (paragraph 3); Results/Evaluation of computational resources on species level queries (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 | Strain level microbial detection and quantification with applications to single cell metagenomics Methods (paragraph 7); Methods (paragraph 1) Version: version of record | 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","Kraken2","Taxonomic assignments"] Individual claims | Strain level microbial detection and quantification with applications to single cell metagenomics Methods (paragraph 7); Methods (paragraph 1) Version: version of record | 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 | Strain level microbial detection and quantification with applications to single cell metagenomics Methods (paragraph 7); Methods (paragraph 1) Version: version of record | 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 | Strain level microbial detection and quantification with applications to single cell metagenomics Methods (paragraph 7); Methods (paragraph 1) Version: version of record | 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 | Strain level microbial detection and quantification with applications to single cell metagenomics Results/Precision and recall in read classification across all species level queries (paragraph 3); Results/Evaluation of computational resources on species level queries (paragraph 1) Version: version of record | 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 | Strain level microbial detection and quantification with applications to single cell metagenomics Introduction (paragraph 4); Results/Precision and recall in read classification across all species level queries (paragraph 3) Version: version of record | 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 | Strain level microbial detection and quantification with applications to single cell metagenomics Results/Performance of CAMMiQ on real single-cell metatranscriptomic queries (paragraph 5); Introduction (paragraph 4) Version: version of record | 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 | Strain level microbial detection and quantification with applications to single cell metagenomics Methods/CAMMiQ Index/Sparsifying unique substrings (paragraph 1); Methods/Query processing stage 2: ILP formulation (paragraph 4) Version: version of record | 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 Kraken2 is the comparison-table label; that label does not specify an immutable weight revision. Individual claims | Strain level microbial detection and quantification with applications to single cell metagenomics Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. Version: version of record | 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
- Strain level microbial detection and quantification with applications to single cell metagenomics · Original source · version of record
- DerrickWood/kraken2 README.md · Original source · 8c190b1b668825935dbf6dee5f969227dc8269bb
- DerrickWood/kraken2 LICENSE · Original source · 8c190b1b668825935dbf6dee5f969227dc8269bb
Technical metadata and extraction receipts
Stable ID: reported-model-70f57ebb163a5c
- 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: cammiq-2022; evidence-reported-base-kraken2-readme-md; source locator: Methods (paragraph 7); Methods (paragraph 1) | README.md model description | Introduction (paragraph 3); Introduction (paragraph 4); 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.