Model type
Study-specific predictive method; this record is the paper-specific evaluated configuration.
Configuration
Lemur
Lemur profiles taxonomy from long-read shotgun metagenomic data using marker genes.
Sources
Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Abstract (paragraph 1); Introduction (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
Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Abstract (paragraph 1); Methods/Competitive read alignment with Magnet (paragraph 1)At a glance
Biological inputs
Long-read shotgun metagenomic reads and a marker-gene database
Sources
Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Abstract (paragraph 1); Introduction (paragraph 3)Outputs
Taxonomic profiles
Sources
Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Methods/Synthetic and simulated datasets/Zymo Fecal Reference with TruMatrix (paragraph 1); Results/Chicken gut metagenome (paragraph 2)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 |
|---|---|---|
| Lemur: Long-read taxonomic profiling Mean across five replicate runs on Zymo LOG 10%. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.376 F1 Unit: unitless · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedLightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Table 3, LOG 10% / Lemur row, F1 column Source checking is not independent reproduction. |
How it works
How the evaluated method works
A marker-gene matching procedure and expectation–maximisation reduce false-positive taxonomic calls while retaining supported taxa. Magnet is a separate whole-genome verification tool.
Sources
Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Abstract (paragraph 1); Methods/Competitive read alignment with Magnet (paragraph 1)What was evaluated
The linked evaluation record identifies Lemur: Long-read taxonomic profiling. Its dataset, split, adaptation and evidence origin remain attached to the reported results.
Sources
Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-b3-031Strengths and limitations
Strengths and considerations
- Designed for long-read data with a compact marker reference.
Sources
Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Discussion (paragraph 4); Results/Computational performance (paragraph 3)
Limitations and conditions
- Lemur profiles and Magnet presence/absence validation are separate procedures; one tool’s results should not be assigned to the other.
Sources
Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Introduction (paragraph 3); Results/Method overview (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-6ac0730e8481deSpecifications
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.SourcesLightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Abstract (paragraph 1); Methods/Competitive read alignment with Magnet (paragraph 1) |
| Architecture / procedure | A marker-gene matching procedure and expectation–maximisation reduce false-positive taxonomic calls while retaining supported taxa. Magnet is a separate whole-genome verification tool.SourcesLightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Abstract (paragraph 1); Methods/Competitive read alignment with Magnet (paragraph 1) |
| Biological inputs | Long-read shotgun metagenomic reads and a marker-gene databaseSourcesLightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Abstract (paragraph 1); Introduction (paragraph 3) |
| Outputs | Taxonomic profilesSourcesLightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Methods/Synthetic and simulated datasets/Zymo Fecal Reference with TruMatrix (paragraph 1); Results/Chicken gut metagenome (paragraph 2) |
| Parameters | An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. · Not reported in inspected sourcesSources (2)Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet; treangenlab/lemur README.md · Results/Method overview; Methods/Lemur; Methods/Competitive read alignment with Magnet; Methods/Method Comparison; Methods/Synthetic and simulated datasets/Simulated data from (Dilthey et al. 2019); Methods/Synthetic and simulated datasets/Zymo EVEN & Zymo LOG; Methods/Synthetic and simulated datasets/Simulated metagenome; Methods/Synthetic and simulated datasets/Zymo Fecal Reference with TruMatrix; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision |
| Known versions / configuration | Lemur is the comparison-table label; that label does not specify an immutable weight revision. · Not reported in inspected sourcesSourcesLightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. |
| Training data / fitting | The paper’s approximately 4-GB marker database contains information from more than 300,000 RefSeq genomes; this is a reference index rather than neural pretraining.SourcesLightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Methods/Synthetic and simulated datasets/Simulated data from (Dilthey et al. 2019) (paragraph 1); Methods/Competitive read alignment with Magnet (paragraph 1) |
| 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 applicableSourcesLightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Methods/Competitive read alignment with Magnet (paragraph 1); Discussion (paragraph 2) |
| Access | Official study implementation and usage documentation: https://github.com/treangenlab/lemur/blob/eda2cb57727b72fc5b1fb28be1fe45a4826100f9/README.md. This pinned documentation revision is not automatically the evaluated weight revision.Sourcestreangenlab/lemur 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).Sourcestreangenlab/lemur 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 sourcesSourcestreangenlab/lemur 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 | Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet Abstract (paragraph 1); Methods/Competitive read alignment with Magnet (paragraph 1) Version: PMC archival version PMC11185576.2 | 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 ["Long-read shotgun metagenomic reads and a marker-gene database","Lemur","Taxonomic profiles"] Individual claims | Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet Abstract (paragraph 1); Methods/Competitive read alignment with Magnet (paragraph 1) Version: PMC archival version PMC11185576.2 | 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 | Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet Abstract (paragraph 1); Methods/Competitive read alignment with Magnet (paragraph 1) Version: PMC archival version PMC11185576.2 | 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 | Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet Abstract (paragraph 1); Methods/Competitive read alignment with Magnet (paragraph 1) Version: PMC archival version PMC11185576.2 | 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 A marker-gene matching procedure and expectation–maximisation reduce false-positive taxonomic calls while retaining supported taxa. Magnet is a separate whole-genome verification tool. Individual claims | Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet Abstract (paragraph 1); Methods/Competitive read alignment with Magnet (paragraph 1) Version: PMC archival version PMC11185576.2 | 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 | treangenlab/lemur README.md README.md; checkpoint/access documentation and licence scope Version: eda2cb57727b72fc5b1fb28be1fe45a4826100f9 | 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 Long-read shotgun metagenomic reads and a marker-gene database Individual claims | Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet Abstract (paragraph 1); Introduction (paragraph 3) Version: PMC archival version PMC11185576.2 | 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 profiles Individual claims | Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet Methods/Synthetic and simulated datasets/Zymo Fecal Reference with TruMatrix (paragraph 1); Results/Chicken gut metagenome (paragraph 2) Version: PMC archival version PMC11185576.2 | 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 | treangenlab/lemur README.md Results/Method overview; Methods/Lemur; Methods/Competitive read alignment with Magnet; Methods/Method Comparison; Methods/Synthetic and simulated datasets/Simulated data from (Dilthey et al. 2019); Methods/Synthetic and simulated datasets/Zymo EVEN & Zymo LOG; Methods/Synthetic and simulated datasets/Simulated metagenome; Methods/Synthetic and simulated datasets/Zymo Fecal Reference with TruMatrix; 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: eda2cb57727b72fc5b1fb28be1fe45a4826100f9 | 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 | Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet Results/Method overview; Methods/Lemur; Methods/Competitive read alignment with Magnet; Methods/Method Comparison; Methods/Synthetic and simulated datasets/Simulated data from (Dilthey et al. 2019); Methods/Synthetic and simulated datasets/Zymo EVEN & Zymo LOG; Methods/Synthetic and simulated datasets/Simulated metagenome; Methods/Synthetic and simulated datasets/Zymo Fecal Reference with TruMatrix; 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: PMC archival version PMC11185576.2 | 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
- Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet · Original source · PMC archival version PMC11185576.2
- treangenlab/lemur README.md · Original source · eda2cb57727b72fc5b1fb28be1fe45a4826100f9
- treangenlab/lemur LICENSE · Original source · eda2cb57727b72fc5b1fb28be1fe45a4826100f9
Technical metadata and extraction receipts
Stable ID: reported-model-6ac0730e8481de
- areas
- microbes-communities
- entity level
- method
- version
- Not reported
- reported name
- Lemur
- 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: lemur-magnet-2024; source locator: Abstract (paragraph 1); Methods/Competitive read alignment with Magnet (paragraph 1) | Abstract (paragraph 1); Introduction (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.