Model type
Study-specific predictive method; this record is the paper-specific evaluated configuration.
Configuration
VIBRANT
This viral-contig detector is compared on simulated metagenomes with varying taxonomic composition and complexity.
Sources
Simulation study and comparative evaluation of viral contiguous sequence identification tools · Conclusion (paragraph 1); Methods/Building simulated Illumina metagenomes (paragraph 3)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
Simulation study and comparative evaluation of viral contiguous sequence identification tools · Methods/Tools used in simulation study (paragraph 1); Methods/Tool performance scoring (paragraph 1)At a glance
Biological inputs
Metagenomic contigs
Sources
Simulation study and comparative evaluation of viral contiguous sequence identification tools · Methods/Building simulated Illumina metagenomes (paragraph 3); Results/Tool performance by contig length (paragraph 1)Outputs
Viral-contig or prophage predictions
Sources
Simulation study and comparative evaluation of viral contiguous sequence identification tools · Results/Prophage identification performance (paragraph 1); Discussion (paragraph 1)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 |
|---|---|---|
| VIBRANT: Simulated prophage-contig detection Configuration: VIBRANTTask: Simulated prophage-contig detectionDataset: 20 medium/high-complexity viral simulations Average across twenty medium- and high-complexity simulated communities. Independent external evaluation · Evaluation metadata: needs review | ||
| 0.169 Average prophage F1 Unit: unitless · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedSimulation study and comparative evaluation of viral contiguous sequence identification tools · Table 3, Vibrant row, Prophage F1 column Source checking is not independent reproduction. |
How it works
How the evaluated method works
The benchmark runs existing viral-identification tools on assembled contigs and evaluates both standalone viruses and integrated prophages.
Sources
Simulation study and comparative evaluation of viral contiguous sequence identification tools · Methods/Tools used in simulation study (paragraph 1); Methods/Tool performance scoring (paragraph 1)What was evaluated
The linked evaluation record identifies VIBRANT: Simulated prophage-contig detection. Its dataset, split, adaptation and evidence origin remain attached to the reported results.
Sources
Simulation study and comparative evaluation of viral contiguous sequence identification tools · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-b3-025Strengths and limitations
Strengths and considerations
- Uses several simulation conditions and separately examines integrated viral sequences.
Sources
Simulation study and comparative evaluation of viral contiguous sequence identification tools · Discussion (paragraph 4); Results/Overall tool performance (paragraph 1)
Limitations and conditions
- Sensitivity and false-positive behaviour depend on contig length, community composition and reference coverage.
Sources
Simulation study and comparative evaluation of viral contiguous sequence identification tools · Methods/Building simulated Illumina metagenomes (paragraph 4); Results/Tool performance by contig length (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-27dca28a87cf3cSpecifications
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.SourcesSimulation study and comparative evaluation of viral contiguous sequence identification tools · Methods/Tools used in simulation study (paragraph 1); Methods/Tool performance scoring (paragraph 1) |
| Architecture / procedure | The benchmark runs existing viral-identification tools on assembled contigs and evaluates both standalone viruses and integrated prophages.SourcesSimulation study and comparative evaluation of viral contiguous sequence identification tools · Methods/Tools used in simulation study (paragraph 1); Methods/Tool performance scoring (paragraph 1) |
| Biological inputs | Metagenomic contigsSourcesSimulation study and comparative evaluation of viral contiguous sequence identification tools · Methods/Building simulated Illumina metagenomes (paragraph 3); Results/Tool performance by contig length (paragraph 1) |
| Outputs | Viral-contig or prophage predictionsSourcesSimulation study and comparative evaluation of viral contiguous sequence identification tools · Results/Prophage identification performance (paragraph 1); Discussion (paragraph 1) |
| Parameters | An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. · Not reported in inspected sourcesSources (2)Simulation study and comparative evaluation of viral contiguous sequence identification tools; Strong-Lab/Viral_Classification_in_Metagenomics README.md · Methods/Phybrid, a hybrid gene content and nucleotide feature set for viral classification; Methods/Gene content feature set creation; Methods/Model and hyperparameter selection; Methods/Building simulated Illumina metagenomes; Methods/Integrated prophage identification; Methods/Tools used in simulation study; Methods/Tool performance scoring; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision |
| Known versions / configuration | VIBRANT is the comparison-table label; that label does not specify an immutable weight revision. · Not reported in inspected sourcesSourcesSimulation study and comparative evaluation of viral contiguous sequence identification tools · Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. |
| Training data / fitting | The study evaluates released software on simulated assembled contigs, rather than fitting this comparator on the study’s labels. The exact upstream training/reference inventory is not restated.SourcesSimulation study and comparative evaluation of viral contiguous sequence identification tools · Methods / Tools used in simulation study |
| Context limits | A maximum input/context length for this exact evaluated configuration is not established by the inspected sources. · Not reported in inspected sourcesSources (2)Simulation study and comparative evaluation of viral contiguous sequence identification tools; Strong-Lab/Viral_Classification_in_Metagenomics README.md · Methods/Phybrid, a hybrid gene content and nucleotide feature set for viral classification; Methods/Gene content feature set creation; Methods/Model and hyperparameter selection; Methods/Building simulated Illumina metagenomes; Methods/Integrated prophage identification; Methods/Tools used in simulation study; Methods/Tool performance scoring; inspected for explicit maximum input length (dataset lengths and family-wide limits are not substituted); README.md at pinned repository revision |
| Access | Official study implementation and usage documentation: https://github.com/Strong-Lab/Viral_Classification_in_Metagenomics/blob/f583cbff6b022ce3a7e3870003e22e14769566fa/README.md. This pinned documentation revision is not automatically the evaluated weight revision.SourcesStrong-Lab/Viral_Classification_in_Metagenomics README.md · README.md; installation, model download and usage instructions |
| Code licence | MIT (study repository code at the cited revision; this does not establish every dependency or historical checkpoint licence).SourcesStrong-Lab/Viral_Classification_in_Metagenomics 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 sourcesSourcesStrong-Lab/Viral_Classification_in_Metagenomics 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.
21 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 | Simulation study and comparative evaluation of viral contiguous sequence identification tools Methods/Tools used in simulation study (paragraph 1); Methods/Tool performance scoring (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 contigs","VIBRANT","Viral-contig or prophage predictions"] Individual claims | Simulation study and comparative evaluation of viral contiguous sequence identification tools Methods/Tools used in simulation study (paragraph 1); Methods/Tool performance scoring (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 | Simulation study and comparative evaluation of viral contiguous sequence identification tools Methods/Tools used in simulation study (paragraph 1); Methods/Tool performance scoring (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 Study-specific predictive method; this record is the paper-specific evaluated configuration. Individual claims | Simulation study and comparative evaluation of viral contiguous sequence identification tools Methods/Tools used in simulation study (paragraph 1); Methods/Tool performance scoring (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 |
| Architecture / procedure The benchmark runs existing viral-identification tools on assembled contigs and evaluates both standalone viruses and integrated prophages. Individual claims | Simulation study and comparative evaluation of viral contiguous sequence identification tools Methods/Tools used in simulation study (paragraph 1); Methods/Tool performance scoring (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 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 | Strong-Lab/Viral_Classification_in_Metagenomics README.md README.md; checkpoint/access documentation and licence scope Version: f583cbff6b022ce3a7e3870003e22e14769566fa | 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 Metagenomic contigs Individual claims | Simulation study and comparative evaluation of viral contiguous sequence identification tools Methods/Building simulated Illumina metagenomes (paragraph 3); Results/Tool performance by contig length (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 |
| Outputs Viral-contig or prophage predictions Individual claims | Simulation study and comparative evaluation of viral contiguous sequence identification tools Results/Prophage identification performance (paragraph 1); Discussion (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 |
| Parameters An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. Individual claims | Strong-Lab/Viral_Classification_in_Metagenomics README.md Methods/Phybrid, a hybrid gene content and nucleotide feature set for viral classification; Methods/Gene content feature set creation; Methods/Model and hyperparameter selection; Methods/Building simulated Illumina metagenomes; Methods/Integrated prophage identification; Methods/Tools used in simulation study; Methods/Tool performance scoring; 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: f583cbff6b022ce3a7e3870003e22e14769566fa | 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 | Simulation study and comparative evaluation of viral contiguous sequence identification tools Methods/Phybrid, a hybrid gene content and nucleotide feature set for viral classification; Methods/Gene content feature set creation; Methods/Model and hyperparameter selection; Methods/Building simulated Illumina metagenomes; Methods/Integrated prophage identification; Methods/Tools used in simulation study; Methods/Tool performance scoring; 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: 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
- Simulation study and comparative evaluation of viral contiguous sequence identification tools · Original source · version of record
- Strong-Lab/Viral_Classification_in_Metagenomics README.md · Original source · f583cbff6b022ce3a7e3870003e22e14769566fa
- Strong-Lab/Viral_Classification_in_Metagenomics LICENSE · Original source · f583cbff6b022ce3a7e3870003e22e14769566fa
Technical metadata and extraction receipts
Stable ID: reported-model-27dca28a87cf3c
- areas
- microbes-communities
- entity level
- method
- version
- Not reported
- reported name
- VIBRANT
- 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: viral-contig-simulation-2021; source locator: Methods/Tools used in simulation study (paragraph 1); Methods/Tool performance scoring (paragraph 1) | Conclusion (paragraph 1); Methods/Building simulated Illumina metagenomes (paragraph 3); 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.