Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Protocol
Species profiling on Dilthey2019 simulated long reads (Long-read taxonomic profiling)
Species profiling on Dilthey2019 simulated long reads · Table 1:. Species-level recall/precision/F 1. MetaMaps results copied from original manuscript; other tool versions reported in Methods. 200,114 reads;96 strain design,94 strains with RefSeq species representatives; average read 4,997 bp.
Sources
Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Table 1:: Recall, Species profiling on Dilthey2019 simulated long readsOverview
Key specifications have not been extracted for this record. See the linked evaluation and sources for the reported setup.
limited source coverage · Automated source review, 2026-09-17. All specifications and missing details
Results
Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.
Species profiling on Dilthey2019 simulated long reads · Table 1:
Recall (fraction) · Higher values are better.
Species profiling on Dilthey2019 simulated long reads (Long-read taxonomic profiling) · Species profiling on Dilthey2019 simulated long reads
Evidence origin: Author-reported evaluation, Independent external evaluation, Result quoted from another source.
Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Table 1:: Recall, Species profiling on Dilthey2019 simulated long reads- MetaMaps is quoted prior evidence, not an independent repeated run.
- Reference databases and classifier-versus-profiler task differ.
Comparison details and limitations
Species-level recall/precision/F 1. MetaMaps results copied from original manuscript; other tool versions reported in Methods. 200,114 reads;96 strain design,94 strains with RefSeq species representatives; average read 4,997 bp.
- No interval assigned unless printed in source cell.
Automated source review: 2026-09-17. Numerical source review does not establish independent reproduction.
Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.
Showing 7 of 7 matching rows.
Methods and evaluation design
Procedure, tasks and evaluated configurations
How it works
Evaluation in this paper
Species-level recall/precision/F 1. MetaMaps results copied from original manuscript; other tool versions reported in Methods. 200,114 reads;96 strain design,94 strains with RefSeq species representatives; average read 4,997 bp.
Sources
Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Table 1:: Recall, Species profiling on Dilthey2019 simulated long readsEvaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
These source-backed links do not make different protocols or scores interchangeable.
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- Lemur: Species profiling on Dilthey2019 simulated long reads
- Lemur + Magnet: Species profiling on Dilthey2019 simulated long reads
- Centrifuger: Species profiling on Dilthey2019 simulated long reads
- Kraken 2: Species profiling on Dilthey2019 simulated long reads
- Melon: Species profiling on Dilthey2019 simulated long reads
- Sourmash: Species profiling on Dilthey2019 simulated long reads
- MetaMaps: Species profiling on Dilthey2019 simulated long reads
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
No reviewed evaluations with results linked in this release.
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
Select a task-valid null control after reviewing inputs and metric
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Select an upstream conventional reference after reviewing the full protocol
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums
Coverage is derived from release 2026-09-29-06401fd5b220. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Strengths, limitations and unresolved questions
Strengths and limitations
Limitations and conditions
No source-reviewed explanatory claims are recorded here yet.
Profile review details
Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.
Stable record: paper-protocol-1080592b8d6a8ce0bdSpecifications
Inputs, training, access and other details
Explanatory profile: limited source coverage · Automated source review, 2026-09-17. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Datasets | Not extracted or verified for this record. |
| Organisms | Not extracted or verified for this record. |
| Assays | Not extracted or verified for this record. |
| Splits | Not extracted or verified for this record. |
| Allowed inputs | Not extracted or verified for this record. |
| Adaptation | Not extracted or verified for this record. |
| Metrics | Not extracted or verified for this record. |
| Baselines | Not extracted or verified for this record. |
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Papers and result coverage
Last literature check: 2026-09-17. Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
| Paper or primary resource | Version | Reference |
|---|---|---|
| Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet | PMC archival version PMC11185576.2 | Read source DOI: 10.1101/2024.06.01.596961 |
Historical gaps recorded on 2026-09-17
The catalogue now holds 21 result rows for this benchmark. A note below about pending extraction describes the state on 2026-09-17 and may since have been answered by a later batch. The result rows and their sources are the current record.
- Independent batch review before import; preserve existing observation identities.
Search and extraction details
complete comparison tables extracted pending publication review
Searches
- Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet primary paper benchmark results
Evidence locations
- Table 1:: Recall, Species profiling on Dilthey2019 simulated long reads
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.
3 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Evaluation in this paper Species-level recall/precision/F 1. MetaMaps results copied from original manuscript; other tool versions reported in Methods. 200,114 reads;96 strain design,94 strains with RefSeq species representatives; average read 4,997 bp. Individual claims | Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet Table 1:: Recall, Species profiling on Dilthey2019 simulated long reads Version: PMC archival version PMC11185576.2 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Introduction Species profiling on Dilthey2019 simulated long reads · Table 1:. Species-level recall/precision/F 1. MetaMaps results copied from original manuscript; other tool versions reported in Methods. 200,114 reads;96 strain design,94 strains with RefSeq species representatives; average read 4,997 bp. Individual claims | Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet Table 1:: Recall, Species profiling on Dilthey2019 simulated long reads Version: PMC archival version PMC11185576.2 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Relationship: evaluates task reported-task-6330d593980b5b Individual claims | Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet Table 1:: Recall, Species profiling on Dilthey2019 simulated long reads Version: PMC archival version PMC11185576.2 | source checked automated source review · 2026-09-17 Audit detailsField: Claim: paper-claim-4e9825e29807055d9c Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: needs review
1 source records and release history
- Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Original source · PMC archival version PMC11185576.2
Technical metadata and extraction receipts
Stable ID: paper-protocol-1080592b8d6a8ce0bd
- areas
- microbes-communities
- tasks
- Long-read taxonomic profiling
- entity level
- protocol
- protocol
- Species-level recall/precision/F 1. MetaMaps results copied from original manuscript; other tool versions reported in Methods. 200,114 reads;96 strain design,94 strains with RefSeq species representatives; average read 4,997 bp.
- comparison panels
- id: part2-lemur-magnet-2024-T1-a3172c2928; title: Species profiling on Dilthey2019 simulated long reads · Table 1:; protocol id: paper-protocol-1080592b8d6a8ce0bd; dataset id: paper-dataset-e8eb310c5d40e647ac; metric: Recall; unit: fraction; direction: higher; result ids: paper-result-80f8cca2c2d9379a1a; paper-result-620e5294f3d001ac96; paper-result-a91cd2aadeccebf9b9; paper-result-b70bf4b4c41e6dd812; paper-result-6da2d59412e925bccd; paper-result-74d2e70b442ba9026b; paper-result-8fd5837795f2fbba5f; source ids: part2-lemur-magnet-2024; source locator: Table 1:: Recall, Species profiling on Dilthey2019 simulated long reads; context: Species-level recall/precision/F 1. MetaMaps results copied from original manuscript; other tool versions reported in Methods. 200,114 reads;96 strain design,94 strains with RefSeq species representatives; average read 4,997 bp.; caveats: MetaMaps is quoted prior evidence, not an independent repeated run.; Reference databases and classifier-versus-profiler task differ.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-lemur-magnet-2024-T1-81ab2d846d; title: Species profiling on Dilthey2019 simulated long reads · Table 1:; protocol id: paper-protocol-1080592b8d6a8ce0bd; dataset id: paper-dataset-e8eb310c5d40e647ac; metric: Precision; unit: fraction; direction: higher; result ids: paper-result-2268ad4341b9316164; paper-result-06a95cb8e4f61822eb; paper-result-9a39bac49d7dcf2b79; paper-result-a6256bb040cd29f64f; paper-result-f53c61bd32688408d8; paper-result-e2ceeb0f245677c087; paper-result-0dc829636e77fc0d92; source ids: part2-lemur-magnet-2024; source locator: Table 1:: Precision, Species profiling on Dilthey2019 simulated long reads; context: Species-level recall/precision/F 1. MetaMaps results copied from original manuscript; other tool versions reported in Methods. 200,114 reads;96 strain design,94 strains with RefSeq species representatives; average read 4,997 bp.; caveats: MetaMaps is quoted prior evidence, not an independent repeated run.; Reference databases and classifier-versus-profiler task differ.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-lemur-magnet-2024-T1-e9572b0ed9; title: Species profiling on Dilthey2019 simulated long reads · Table 1:; protocol id: paper-protocol-1080592b8d6a8ce0bd; dataset id: paper-dataset-e8eb310c5d40e647ac; metric: F1 score; unit: fraction; direction: higher; result ids: paper-result-4468fa08040fb0bd80; paper-result-19f79487e8dff1a781; paper-result-25455d4621f0aeb383; paper-result-f9b8d072704477374e; paper-result-03860ee74178c46356; paper-result-fdc2db2e65a30e98e7; paper-result-f8adf74d2b525a6380; source ids: part2-lemur-magnet-2024; source locator: Table 1:: F1 score, Species profiling on Dilthey2019 simulated long reads; context: Species-level recall/precision/F 1. MetaMaps results copied from original manuscript; other tool versions reported in Methods. 200,114 reads;96 strain design,94 strains with RefSeq species representatives; average read 4,997 bp.; caveats: MetaMaps is quoted prior evidence, not an independent repeated run.; Reference databases and classifier-versus-profiler task differ.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17
- benchmark research
- review date: 2026-09-17; status: complete_comparison_tables_extracted_pending_publication_review; primary sources: part2-lemur-magnet-2024; inspected locators: Table 1:: Recall, Species profiling on Dilthey2019 simulated long reads; searched queries: Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet primary paper benchmark results; gaps: Independent batch review before import; preserve existing observation identities.; claim scope: Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
- legacy kinds
- benchmark
- entity classification
- review date: 2026-09-17; rationale: The source-backed record identifies a specified evaluated procedure and its dataset/split/scoring context. Classify it as a protocol while preserving version and comparison restrictions.; source ids: part2-lemur-magnet-2024; source locator: Table 1:: Recall, Species profiling on Dilthey2019 simulated long reads; ambiguities: None recorded
Related records
- evaluates task: Long-read taxonomic profiling
- subject: Species profiling on Dilthey2019 simulated long reads (Long-read taxonomic profiling): links:evaluates_task:reported-task-6330d593980b5b
- benchmark: Lemur: Species profiling on Dilthey2019 simulated long reads
- benchmark: Lemur + Magnet: Species profiling on Dilthey2019 simulated long reads
- benchmark: Centrifuger: Species profiling on Dilthey2019 simulated long reads
- benchmark: Kraken 2: Species profiling on Dilthey2019 simulated long reads
- benchmark: Melon: Species profiling on Dilthey2019 simulated long reads
- benchmark: Sourmash: Species profiling on Dilthey2019 simulated long reads
- benchmark: MetaMaps: Species profiling on Dilthey2019 simulated long reads