Model type
Study-specific predictive method; this record is the paper-specific evaluated configuration.
Configuration
NABAS+
NABAS+ performs species-level profiling of Illumina shotgun reads through reference alignment and stringent filtering.
Sources
Advancing metagenomic classification with NABAS+: a novel alignment-based approach · Introduction (paragraph 3); Materials and methods/Statistical comparison and visualization (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
Advancing metagenomic classification with NABAS+: a novel alignment-based approach · Materials and methods/Datasets and reference databases/CAMI samples (paragraph 3); Materials and methods/Running the classifiers (paragraph 2)At a glance
Biological inputs
Illumina shotgun metagenomic reads and a curated species reference database
Sources
Advancing metagenomic classification with NABAS+: a novel alignment-based approach · Introduction (paragraph 3); Discussion (paragraph 6)Outputs
Species identifications and microbiome profiles
Sources
Advancing metagenomic classification with NABAS+: a novel alignment-based approach · Materials and methods/Statistical comparison and visualization (paragraph 7); Discussion (paragraph 5)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 |
|---|---|---|
| NABAS+: Metagenomic taxonomic classification Configuration: NABAS+Task: Metagenomic taxonomic classificationDataset: CAMI II Toy human gastrooral sample19-new Newly generated sample19 used for classifier comparison. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.719 F1 score Unit: unitless · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Table 3, Sample19-new / NABAS+ row, F1 score column Source checking is not independent reproduction. |
How it works
How the evaluated method works
BWA aligns reads to a curated RefSeq database with one selected genome per species. Quality filters retain genomes supported by reliable mapped reads.
Sources
Advancing metagenomic classification with NABAS+: a novel alignment-based approach · Materials and methods/Datasets and reference databases/CAMI samples (paragraph 3); Materials and methods/Running the classifiers (paragraph 2)What was evaluated
The linked evaluation record identifies NABAS+: Metagenomic taxonomic classification. Its dataset, split, adaptation and evidence origin remain attached to the reported results.
Sources
Advancing metagenomic classification with NABAS+: a novel alignment-based approach · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-039Strengths and limitations
Strengths and considerations
- Tests simulated gastrooral communities and deeply sequenced microbial standards.
Sources
Advancing metagenomic classification with NABAS+: a novel alignment-based approach · Abstract (paragraph 1); Materials and methods/Datasets and reference databases/Zymo community standards (paragraph 1)
Limitations and conditions
- Alignment and reference curation trade computational cost against precision; retrospective pathogen examples do not establish clinical diagnostic performance.
Sources
Advancing metagenomic classification with NABAS+: a novel alignment-based approach · Results/Testing classifiers on the CAMI gastrooral in silico data (paragraph 2); Materials and methods/Statistical comparison and visualization (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-e7d203bd99ca99Specifications
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 | Study-specific predictive method; this record is the paper-specific evaluated configuration.SourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Materials and methods/Datasets and reference databases/CAMI samples (paragraph 3); Materials and methods/Running the classifiers (paragraph 2) |
| Architecture / procedure | BWA aligns reads to a curated RefSeq database with one selected genome per species. Quality filters retain genomes supported by reliable mapped reads.SourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Materials and methods/Datasets and reference databases/CAMI samples (paragraph 3); Materials and methods/Running the classifiers (paragraph 2) |
| Biological inputs | Illumina shotgun metagenomic reads and a curated species reference databaseSourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Introduction (paragraph 3); Discussion (paragraph 6) |
| Outputs | Species identifications and microbiome profilesSourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Materials and methods/Statistical comparison and visualization (paragraph 7); Discussion (paragraph 5) |
| Parameters | An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. · Not reported in inspected sourcesSources (2)Advancing metagenomic classification with NABAS+: a novel alignment-based approach; TakacsBertalan/NABAS_paper_scripts README.md · Materials and methods/Selecting and setting up classifiers for the initial gut metagenome analysis; Materials and methods/Selecting and setting up reference classifiers for NABAS+ benchmarking; Materials and methods/Datasets and reference databases/Human gut microbiome samples: acquisition and sequencing; Materials and methods/Datasets and reference databases/Consent for sample collection; Materials and methods/Datasets and reference databases/Real-world clinical dataset; Materials and methods/Datasets and reference databases/CAMI samples; Materials and methods/Datasets and reference databases/Recreating the CAMI sample19; Materials and methods/Datasets and reference databases/Zymo community standards; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision |
| Known versions / configuration | NABAS+ is the comparison-table label; that label does not specify an immutable weight revision. · Not reported in inspected sourcesSourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. |
| Training data / fitting | Reference-genome curation rather than learned neural weights.SourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Materials and methods/Datasets and reference databases/Recreating the CAMI sample19 (paragraph 1); Materials and methods/Datasets and reference databases/CAMI samples (paragraph 3) |
| 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 applicableSourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Materials and methods/Datasets and reference databases/CAMI samples (paragraph 3); Discussion (paragraph 6) |
| Access | Official study implementation and usage documentation: https://github.com/TakacsBertalan/NABAS_paper_scripts/blob/7cab4d317a2c362988e7b96fb33f92a9c79a9fdc/README.md. This pinned documentation revision is not automatically the evaluated weight revision.SourcesTakacsBertalan/NABAS_paper_scripts README.md · README.md; installation, model download and usage instructions |
| Code licence | CC BY-NC 4.0 (study repository code at the cited revision; this does not establish every dependency or historical checkpoint licence).SourcesTakacsBertalan/NABAS_paper_scripts LICENSE · LICENSE; complete licence text |
| Weights licence | The inspected model-access documentation does not explicitly identify terms for this exact evaluated checkpoint or fitted head; repository code terms are shown separately. · Not reported in inspected sourcesSourcesTakacsBertalan/NABAS_paper_scripts README.md · README.md; checkpoint/access documentation and licence scope |
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 | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Materials and methods/Datasets and reference databases/CAMI samples (paragraph 3); Materials and methods/Running the classifiers (paragraph 2) Version: PMC12231603.1 | 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 ["Illumina shotgun metagenomic reads and a curated species reference database","NABAS+","Species identifications and microbiome profiles"] Individual claims | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Materials and methods/Datasets and reference databases/CAMI samples (paragraph 3); Materials and methods/Running the classifiers (paragraph 2) Version: PMC12231603.1 | 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 | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Materials and methods/Datasets and reference databases/CAMI samples (paragraph 3); Materials and methods/Running the classifiers (paragraph 2) Version: PMC12231603.1 | 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 Study-specific predictive method; this record is the paper-specific evaluated configuration. Individual claims | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Materials and methods/Datasets and reference databases/CAMI samples (paragraph 3); Materials and methods/Running the classifiers (paragraph 2) Version: PMC12231603.1 | 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 BWA aligns reads to a curated RefSeq database with one selected genome per species. Quality filters retain genomes supported by reliable mapped reads. Individual claims | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Materials and methods/Datasets and reference databases/CAMI samples (paragraph 3); Materials and methods/Running the classifiers (paragraph 2) Version: PMC12231603.1 | 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 The inspected model-access documentation does not explicitly identify terms for this exact evaluated checkpoint or fitted head; repository code terms are shown separately. Individual claims | TakacsBertalan/NABAS_paper_scripts README.md README.md; checkpoint/access documentation and licence scope Version: 7cab4d317a2c362988e7b96fb33f92a9c79a9fdc | 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 |
| Biological inputs Illumina shotgun metagenomic reads and a curated species reference database Individual claims | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Introduction (paragraph 3); Discussion (paragraph 6) Version: PMC12231603.1 | 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 Species identifications and microbiome profiles Individual claims | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Materials and methods/Statistical comparison and visualization (paragraph 7); Discussion (paragraph 5) Version: PMC12231603.1 | 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 An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. Individual claims | TakacsBertalan/NABAS_paper_scripts README.md Materials and methods/Selecting and setting up classifiers for the initial gut metagenome analysis; Materials and methods/Selecting and setting up reference classifiers for NABAS+ benchmarking; Materials and methods/Datasets and reference databases/Human gut microbiome samples: acquisition and sequencing; Materials and methods/Datasets and reference databases/Consent for sample collection; Materials and methods/Datasets and reference databases/Real-world clinical dataset; Materials and methods/Datasets and reference databases/CAMI samples; Materials and methods/Datasets and reference databases/Recreating the CAMI sample19; Materials and methods/Datasets and reference databases/Zymo community standards; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 7cab4d317a2c362988e7b96fb33f92a9c79a9fdc | 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 |
| Parameters An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. Individual claims | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Materials and methods/Selecting and setting up classifiers for the initial gut metagenome analysis; Materials and methods/Selecting and setting up reference classifiers for NABAS+ benchmarking; Materials and methods/Datasets and reference databases/Human gut microbiome samples: acquisition and sequencing; Materials and methods/Datasets and reference databases/Consent for sample collection; Materials and methods/Datasets and reference databases/Real-world clinical dataset; Materials and methods/Datasets and reference databases/CAMI samples; Materials and methods/Datasets and reference databases/Recreating the CAMI sample19; Materials and methods/Datasets and reference databases/Zymo community standards; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12231603.1 | 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
- Advancing metagenomic classification with NABAS+: a novel alignment-based approach · Original source · PMC12231603.1
- TakacsBertalan/NABAS_paper_scripts README.md · Original source · 7cab4d317a2c362988e7b96fb33f92a9c79a9fdc
- TakacsBertalan/NABAS_paper_scripts LICENSE · Original source · 7cab4d317a2c362988e7b96fb33f92a9c79a9fdc
Technical metadata and extraction receipts
Stable ID: reported-model-e7d203bd99ca99
- areas
- microbes-communities
- entity level
- method
- version
- Not reported
- reported name
- NABAS+
- 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: nabas-plus-2025; source locator: Materials and methods/Datasets and reference databases/CAMI samples (paragraph 3); Materials and methods/Running the classifiers (paragraph 2) | Introduction (paragraph 3); Materials and methods/Statistical comparison and visualization (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.