Strain-level taxonomic abundance estimation is compared against known compositions in simulated human-gut read collections.
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 | Queries derived from a reference index of human-gut bacterial genomes; Table 5 reports four strain-level query sets.SourcesStrain level microbial detection and quantification with applications to single cell metagenomics · Results: Datasets; Performance of CAMMiQ at the strain level; Table 5; cached text lines 19–22, 55–57 |
| Splits | An index-and-query benchmark rather than a supervised train/test split; the relevant evaluation is the strain-level collection.SourcesStrain level microbial detection and quantification with applications to single cell metagenomics · Results: Datasets; Performance of CAMMiQ at the strain level; Table 5; cached text lines 19–22, 55–57 |
| Metrics | Correctly identified strains and L1/L2 distances between predicted and true relative abundance vectors.SourcesStrain level microbial detection and quantification with applications to single cell metagenomics · Results: Datasets; Performance of CAMMiQ at the strain level; Table 5; cached text lines 19–22, 55–57 |
| Baselines | Kraken2, KrakenUniq, CLARK, Centrifuge and MetaPhlAn2.SourcesStrain level microbial detection and quantification with applications to single cell metagenomics · Results: Datasets; Performance of CAMMiQ at the strain level; Table 5; cached text lines 19–22, 55–57 |
| Leakage controls | The four strain-level queries are simulated from the same 614-genome reference collection used to build the custom indices. A genome without unique or doubly unique 100-mers is excluded from query generation. This is identification and abundance estimation against an indexed collection, not a strain-held-out generalization test.Sources (2)Strain level microbial detection and quantification with applications to single cell metagenomics; cammiq-2022__41467_2022_33869_MOESM1_ESM.pdf · Supplementary Notes 5.2 Strain-Level Index Dataset and 5.5 Strain-Level Queries |
| Uncertainty | Table 5 reports one identification count and L1/L2 abundance error for each of four different query constructions. Supplementary Note 5.5 does not define these four constructions as replicate draws for a confidence interval, and no uncertainty interval accompanies the table values. · Not reported in inspected sourcesSources (2)Strain level microbial detection and quantification with applications to single cell metagenomics; cammiq-2022__41467_2022_33869_MOESM1_ESM.pdf · Table 5; Supplementary Note 5.5 Strain-Level Queries |
| Entity type | Paper-specific computational evaluation protocol.SourcesStrain level microbial detection and quantification with applications to single cell metagenomics · Results: Datasets; Performance of CAMMiQ at the strain level; Table 5; cached text lines 19–22, 55–57 |
| Organisms | Human-gut bacterial strains.SourcesStrain level microbial detection and quantification with applications to single cell metagenomics · Results: Datasets; Performance of CAMMiQ at the strain level; Table 5; cached text lines 19–22, 55–57 |
| Assays | Synthetic sequence queries with known strain abundances.SourcesStrain level microbial detection and quantification with applications to single cell metagenomics · Results: Datasets; Performance of CAMMiQ at the strain level; Table 5; cached text lines 19–22, 55–57 |
| Allowed inputs | Metagenomic reads and a reference genome index.SourcesStrain level microbial detection and quantification with applications to single cell metagenomics · Results: Datasets; Performance of CAMMiQ at the strain level; Table 5; cached text lines 19–22, 55–57 |
| Adaptation | Reference-index construction and query classification; no assay-label supervised fitting is prescribed.SourcesStrain level microbial detection and quantification with applications to single cell metagenomics · Results: Datasets; Performance of CAMMiQ at the strain level; Table 5; cached text lines 19–22, 55–57 |
Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.
Queries derived from a reference index of human-gut bacterial genomes; Table 5 reports four strain-level query sets. An index-and-query benchmark rather than a supervised train/test split; the relevant evaluation is the strain-level collection. Correctly identified strains and L1/L2 distances between predicted and true relative abundance vectors. Kraken2, KrakenUniq, CLARK, Centrifuge and MetaPhlAn2. The four strain-level queries are simulated from the same 614-genome reference collection used to build the custom indices. A genome without unique or doubly unique 100-mers is excluded from query generation. This is identification and abundance estimation against an indexed collection, not a strain-held-out generalization test.
Each evaluation records what was tested and under which conditions.
Release 2026-09-17-d277315f7d76 · 2 evaluations · 2 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| CAMMiQ: Strain-level abundance quantification Configuration: CAMMiQTask: Strain-level abundance quantificationDataset: HumanGut-all strain-level query Strain-level quantification on the HumanGut-all synthetic query. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.0517 L1 abundance error Unit: unitless · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedStrain level microbial detection and quantification with applications to single cell metagenomics · Table 5, B. L1 Err. / HumanGut-all row, CAMMiQ L1 Err. column Source checking is not independent reproduction. |
| Kraken2: Strain-level abundance quantification Configuration: Kraken2Task: Strain-level abundance quantificationDataset: HumanGut-all strain-level query Strain-level quantification on the HumanGut-all synthetic query. Independent external evaluation · Evaluation metadata: needs review | ||
| 0.2841 L1 abundance error Unit: unitless · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedStrain level microbial detection and quantification with applications to single cell metagenomics · Table 5, B. L1 Err. / HumanGut-all row, Kraken2 L1 Err. column Source checking is not independent reproduction. |
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 |
|---|---|---|
| Strain level microbial detection and quantification with applications to single cell metagenomics | version of record | Read source DOI: 10.1038/s41467-022-33869-7 |
source found structured extraction pending
Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change.
Stable record: reported-task-571f0a2e7faed3Trace 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 summary of the cited evaluation; exact task configuration and source version remain part of the protocol. Individual claims | Strain level microbial detection and quantification with applications to single cell metagenomics Results: Datasets; Performance of CAMMiQ at the strain level; Table 5; cached text lines 19–22, 55–57 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram steps ["Input: Metagenomic reads and a reference genome index.","Evaluation: An index-and-query benchmark rather than a supervised train/test split; the relevant evaluation is the strain-level collection.","Readout: Correctly identified strains and L1/L2 distances between predicted and true relative abundance vectors."] Individual claims | Strain level microbial detection and quantification with applications to single cell metagenomics Results: Datasets; Performance of CAMMiQ at the strain level; Table 5; cached text lines 19–22, 55–57 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Computational evaluation flow Individual claims | Strain level microbial detection and quantification with applications to single cell metagenomics Results: Datasets; Performance of CAMMiQ at the strain level; Table 5; cached text lines 19–22, 55–57 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets Queries derived from a reference index of human-gut bacterial genomes; Table 5 reports four strain-level query sets. Individual claims | Strain level microbial detection and quantification with applications to single cell metagenomics Results: Datasets; Performance of CAMMiQ at the strain level; Table 5; cached text lines 19–22, 55–57 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Splits An index-and-query benchmark rather than a supervised train/test split; the relevant evaluation is the strain-level collection. Individual claims | Strain level microbial detection and quantification with applications to single cell metagenomics Results: Datasets; Performance of CAMMiQ at the strain level; Table 5; cached text lines 19–22, 55–57 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Adaptation Reference-index construction and query classification; no assay-label supervised fitting is prescribed. Individual claims | Strain level microbial detection and quantification with applications to single cell metagenomics Results: Datasets; Performance of CAMMiQ at the strain level; Table 5; cached text lines 19–22, 55–57 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Metrics Correctly identified strains and L1/L2 distances between predicted and true relative abundance vectors. Individual claims | Strain level microbial detection and quantification with applications to single cell metagenomics Results: Datasets; Performance of CAMMiQ at the strain level; Table 5; cached text lines 19–22, 55–57 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Baselines Kraken2, KrakenUniq, CLARK, Centrifuge and MetaPhlAn2. Individual claims | Strain level microbial detection and quantification with applications to single cell metagenomics Results: Datasets; Performance of CAMMiQ at the strain level; Table 5; cached text lines 19–22, 55–57 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Leakage controls The four strain-level queries are simulated from the same 614-genome reference collection used to build the custom indices. A genome without unique or doubly unique 100-mers is excluded from query generation. This is identification and abundance estimation against an indexed collection, not a strain-held-out generalization test. Individual claims | Strain level microbial detection and quantification with applications to single cell metagenomics Supplementary Notes 5.2 Strain-Level Index Dataset and 5.5 Strain-Level Queries Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Leakage controls The four strain-level queries are simulated from the same 614-genome reference collection used to build the custom indices. A genome without unique or doubly unique 100-mers is excluded from query generation. This is identification and abundance estimation against an indexed collection, not a strain-held-out generalization test. Individual claims | cammiq-2022__41467_2022_33869_MOESM1_ESM.pdf Supplementary Notes 5.2 Strain-Level Index Dataset and 5.5 Strain-Level Queries Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved 2026-09-16; sha256:910aed130f3b4648b0758bdcc6b82d1e2d38ddb320ea80d670c98c565930610b | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: 41467_2022_33869_MOESM1_ESM.pdf |
Release 2026-09-17-d277315f7d76 · Record review: needs review
Stable ID: reported-task-571f0a2e7faed3