Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Task
Simulated prophage-contig detection
Simulated metagenome assessment compares viral-contig and prophage identification across varying sample conditions.
Sources
Simulation study and comparative evaluation of viral contiguous sequence identification tools · Discussion and Conclusion; cached text lines 71–74At a glance
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 |
|---|---|
| Datasets | Thirty simulated metagenome collections.SourcesSimulation study and comparative evaluation of viral contiguous sequence identification tools · Discussion and Conclusion; cached text lines 71–74 |
| Splits | Simulation scenarios vary taxonomic complexity and contig characteristics; exact reference withholding remains unextracted.SourcesSimulation study and comparative evaluation of viral contiguous sequence identification tools · Discussion and Conclusion; cached text lines 71–74 |
| Metrics | Precision, F1 and prophage/genus recall are discussed as different outcomes.SourcesSimulation study and comparative evaluation of viral contiguous sequence identification tools · Discussion and Conclusion; cached text lines 71–74 |
| Baselines | Nine viral-identification tools, including Vibrant, VirSorter and Kraken2.SourcesSimulation study and comparative evaluation of viral contiguous sequence identification tools · Discussion and Conclusion; cached text lines 71–74 |
| Leakage controls | Low- and medium-complexity simulation collections use nonoverlapping selected reference genomes. That condition does not establish exclusion from every identification tool’s database.SourcesSimulation study and comparative evaluation of viral contiguous sequence identification tools · Discussion and Conclusion; cached text lines 71–74 |
| Uncertainty | The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim. · Not reported in inspected sourcesSourcesSimulation study and comparative evaluation of viral contiguous sequence identification tools · Discussion and Conclusion; cached text lines 71–74 |
| Entity type | Paper-specific computational evaluation protocol.SourcesSimulation study and comparative evaluation of viral contiguous sequence identification tools · Discussion and Conclusion; cached text lines 71–74 |
| Organisms | Simulated microbial/viral communities.SourcesSimulation study and comparative evaluation of viral contiguous sequence identification tools · Discussion and Conclusion; cached text lines 71–74 |
| Assays | Known-origin simulated contigs.SourcesSimulation study and comparative evaluation of viral contiguous sequence identification tools · Discussion and Conclusion; cached text lines 71–74 |
| Allowed inputs | Assembled contig sequence.SourcesSimulation study and comparative evaluation of viral contiguous sequence identification tools · Discussion and Conclusion; cached text lines 71–74 |
| Adaptation | Existing identification tools are applied across controlled simulation conditions.SourcesSimulation study and comparative evaluation of viral contiguous sequence identification tools · Discussion and Conclusion; cached text lines 71–74 |
How it works
How it worksComputational evaluation flow
Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.
Sources
Simulation study and comparative evaluation of viral contiguous sequence identification tools · Discussion and Conclusion; cached text lines 71–74Evaluation methodology
Thirty simulated metagenome collections. Simulation scenarios vary taxonomic complexity and contig characteristics; exact reference withholding remains unextracted. Precision, F1 and prophage/genus recall are discussed as different outcomes. Nine viral-identification tools, including Vibrant, VirSorter and Kraken2. Low- and medium-complexity simulation collections use nonoverlapping selected reference genomes. That condition does not establish exclusion from every identification tool’s database. The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim.
Sources
Simulation study and comparative evaluation of viral contiguous sequence identification tools · Discussion and Conclusion; cached text lines 71–74Recorded evaluations
Each evaluation records what was tested and under which conditions.
Tested entities and results
Release 2026-09-17-d277315f7d76 · 2 evaluations · 2 metric rows. 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. |
| VirSorter: Simulated prophage-contig detection Configuration: VirSorterTask: 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 | ||
| 0.147 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, VirSorter row, Prophage F1 column Source checking is not independent reproduction. |
Papers and result coverage
Last literature check: 2026-09-17. Primary-paper discovery and source inspection. Source-checked results are not independently reproduced experiments.
| Paper or primary resource | Version | Reference |
|---|---|---|
| Simulation study and comparative evaluation of viral contiguous sequence identification tools | version of record | Read source DOI: 10.1186/s12859-021-04242-0 |
What is still missing
- Performance averages over simulation conditions, not independent training seeds; do not use rank as a probability.
- Benchmark simulation conditions differ from real metagenomic samples.
Search and extraction details
primary comparison table screened
Searches
- "PMC8207588"
Evidence locations
- Table 3
- Methods: Building simulated Illumina metagenomes
Strengths and limitations
Limitations and conditions
- Contig length and taxonomic complexity change performance. The simulation result does not establish generalization to arbitrary real metagenomes or unknown reference families.
Sources
Simulation study and comparative evaluation of viral contiguous sequence identification tools · Discussion and Conclusion; cached text lines 71–74
Profile review details
Task-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced.
Stable record: reported-task-53e3d216eef6dbEvidence 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.
17 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol. Individual claims | Simulation study and comparative evaluation of viral contiguous sequence identification tools Discussion and Conclusion; cached text lines 71–74 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram steps ["Input: Assembled contig sequence.","Evaluation: Existing identification tools are applied across controlled simulation conditions.","Readout: Precision, F1 and prophage/genus recall are discussed as different outcomes."] Individual claims | Simulation study and comparative evaluation of viral contiguous sequence identification tools Discussion and Conclusion; cached text lines 71–74 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Computational evaluation flow Individual claims | Simulation study and comparative evaluation of viral contiguous sequence identification tools Discussion and Conclusion; cached text lines 71–74 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets Thirty simulated metagenome collections. Individual claims | Simulation study and comparative evaluation of viral contiguous sequence identification tools Discussion and Conclusion; cached text lines 71–74 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Splits Simulation scenarios vary taxonomic complexity and contig characteristics; exact reference withholding remains unextracted. Individual claims | Simulation study and comparative evaluation of viral contiguous sequence identification tools Discussion and Conclusion; cached text lines 71–74 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Adaptation Existing identification tools are applied across controlled simulation conditions. Individual claims | Simulation study and comparative evaluation of viral contiguous sequence identification tools Discussion and Conclusion; cached text lines 71–74 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Metrics Precision, F1 and prophage/genus recall are discussed as different outcomes. Individual claims | Simulation study and comparative evaluation of viral contiguous sequence identification tools Discussion and Conclusion; cached text lines 71–74 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Baselines Nine viral-identification tools, including Vibrant, VirSorter and Kraken2. Individual claims | Simulation study and comparative evaluation of viral contiguous sequence identification tools Discussion and Conclusion; cached text lines 71–74 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Leakage controls Low- and medium-complexity simulation collections use nonoverlapping selected reference genomes. That condition does not establish exclusion from every identification tool’s database. Individual claims | Simulation study and comparative evaluation of viral contiguous sequence identification tools Discussion and Conclusion; cached text lines 71–74 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Uncertainty The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim. Individual claims | Simulation study and comparative evaluation of viral contiguous sequence identification tools Discussion and Conclusion; cached text lines 71–74 Version: version of record | unreported automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. 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
2 source records and release history
- Simulation study and comparative evaluation of viral contiguous sequence identification tools · Original source · version of record
- Simulation study and comparative evaluation of viral contiguous sequence identification tools · Original source · version of record
Technical metadata and extraction receipts
Stable ID: reported-task-53e3d216eef6db
- areas
- microbes-communities
- tasks
- Simulated prophage-contig detection
- entity level
- task
- version
- Not reported
- task
- Simulated prophage-contig detection
- scope note
- Paper-specific evaluation task; protocol completeness requires further extraction.
- benchmark research
- review date: 2026-09-17; status: primary_comparison_table_screened; primary sources: expansion-p3-viral-contig-simulation-2021; inspected locators: Table 3; Methods: Building simulated Illumina metagenomes; searched queries: "PMC8207588"; gaps: Performance averages over simulation conditions, not independent training seeds; do not use rank as a probability.; Benchmark simulation conditions differ from real metagenomic samples.; claim scope: Primary-paper discovery and source inspection. Source-checked results are not independently reproduced experiments.
- historical missing metadata
- protocol version: not_reported_in_legacy_extract; split: 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
- benchmark
- entity classification
- review date: 2026-09-17; rationale: This source-scoped record identifies the biological prediction task and holds its paper context. Preserve the existing task identity; exact split, model adaptation and scoring remain in linked evaluations or separate protocol records.; source ids: viral-contig-simulation-2021; source locator: Discussion and Conclusion; cached text lines 71–74; ambiguities: A paper- or suite-specific task may constrain some inputs or metrics; that alone does not make it interchangeable with a complete versioned protocol. No protocol equivalence is inferred.; Some legacy profile Entity type facts use the generic phrase computational evaluation protocol. That boilerplate is not sufficient to establish a single fixed protocol identity or to merge this task with another protocol record.