Model type
Study-specific predictive method; this record is the paper-specific evaluated configuration.
Configuration
CAMMiQ
CAMMiQ identifies and quantifies microbial genomes from metagenomic reads using combinatorial optimisation.
Sources
Strain level microbial detection and quantification with applications to single cell metagenomics · Results/Overview of CAMMiQ indexing and querying procedure (paragraph 3); Methods (paragraph 2)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
Strain level microbial detection and quantification with applications to single cell metagenomics · Methods (paragraph 3); Methods (paragraph 2)At a glance
Biological inputs
Metagenomic reads and a reference-genome index
Sources
Strain level microbial detection and quantification with applications to single cell metagenomics · Results/Precision and recall in read classification across all species level queries (paragraph 2); Methods (paragraph 2)Outputs
Detected reference genomes and relative abundance estimates
Sources
Strain level microbial detection and quantification with applications to single cell metagenomics · Methods (paragraph 4); Results/Overview of CAMMiQ indexing and querying procedure (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 |
|---|---|---|
| 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. |
How it works
How the evaluated method works
An index contains variable-length substrings unique to one reference genome or shared by exactly two. Optimisation resolves the mixture of reference genomes and their abundance from matching reads.
Sources
Strain level microbial detection and quantification with applications to single cell metagenomics · Methods (paragraph 3); Methods (paragraph 2)What was evaluated
The linked evaluation record identifies CAMMiQ: Strain-level abundance quantification. Its dataset, split, adaptation and evidence origin remain attached to the reported results.
Sources
Strain level microbial detection and quantification with applications to single cell metagenomics · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-b3-019Strengths and limitations
Strengths and considerations
- Uses doubly unique substrings to distinguish closely related genomes that share many sequences.
Sources
Strain level microbial detection and quantification with applications to single cell metagenomics · Results/Performance of CAMMiQ on real single-cell metatranscriptomic queries (paragraph 1); Abstract (paragraph 1)
Limitations and conditions
- Identification is relative to the supplied genome database; novel organisms and incomplete references require separate interpretation.
Sources
Strain level microbial detection and quantification with applications to single cell metagenomics · Introduction (paragraph 7); Abstract (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-32a19f43a4c254Specifications
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.SourcesStrain level microbial detection and quantification with applications to single cell metagenomics · Methods (paragraph 3); Methods (paragraph 2) |
| Architecture / procedure | An index contains variable-length substrings unique to one reference genome or shared by exactly two. Optimisation resolves the mixture of reference genomes and their abundance from matching reads.SourcesStrain level microbial detection and quantification with applications to single cell metagenomics · Methods (paragraph 3); Methods (paragraph 2) |
| Biological inputs | Metagenomic reads and a reference-genome indexSourcesStrain level microbial detection and quantification with applications to single cell metagenomics · Results/Precision and recall in read classification across all species level queries (paragraph 2); Methods (paragraph 2) |
| Outputs | Detected reference genomes and relative abundance estimatesSourcesStrain level microbial detection and quantification with applications to single cell metagenomics · Methods (paragraph 4); Results/Overview of CAMMiQ indexing and querying procedure (paragraph 2) |
| Parameters | Not applicable: this is a reference-database algorithm rather than a neural model. · Not applicableSourcesStrain level microbial detection and quantification with applications to single cell metagenomics · Results/Precision and recall in read classification across all species level queries (paragraph 3); Introduction (paragraph 3) |
| Known versions / configuration | CAMMiQ is the comparison-table label; that label does not specify an immutable weight revision. · Not reported in inspected sourcesSourcesStrain level microbial detection and quantification with applications to single cell metagenomics · Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. |
| Training data / fitting | No neural pretraining: the paper builds reference indexes from specified RefSeq releases, including releases 93 and 205.SourcesStrain level microbial detection and quantification with applications to single cell metagenomics · Results/Datasets (paragraph 1); Results/Datasets (paragraph 2) |
| Context limits | Not applicable to a learned context window; the analysed reads/genomes and versioned reference database define the workload. · Not applicableSourcesStrain level microbial detection and quantification with applications to single cell metagenomics · Methods/When to use unique substrings—the error free case/Theorem 1 (paragraph 2); Introduction (paragraph 4) |
| Access | Official study implementation and usage documentation: https://github.com/algo-cancer/CAMMiQ/blob/6142150d427a74cc21a5ee4d8b37a3b78884f163/README.md. This pinned documentation revision is not automatically the evaluated weight revision.Sourcesalgo-cancer/CAMMiQ 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).Sourcesalgo-cancer/CAMMiQ LICENSE · LICENSE; complete licence text |
| Weights licence | Not applicable: this is an indexed combinatorial method, not a pretrained weight release. · Not applicableSourcesStrain level microbial detection and quantification with applications to single cell metagenomics · Methods (paragraph 7); Discussion (paragraph 3) |
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.
19 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 | Strain level microbial detection and quantification with applications to single cell metagenomics Methods (paragraph 3); Methods (paragraph 2) 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 reads and a reference-genome index","CAMMiQ","Detected reference genomes and relative abundance estimates"] Individual claims | Strain level microbial detection and quantification with applications to single cell metagenomics Methods (paragraph 3); Methods (paragraph 2) 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 | Strain level microbial detection and quantification with applications to single cell metagenomics Methods (paragraph 3); Methods (paragraph 2) 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 | Strain level microbial detection and quantification with applications to single cell metagenomics Methods (paragraph 3); Methods (paragraph 2) 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 An index contains variable-length substrings unique to one reference genome or shared by exactly two. Optimisation resolves the mixture of reference genomes and their abundance from matching reads. Individual claims | Strain level microbial detection and quantification with applications to single cell metagenomics Methods (paragraph 3); Methods (paragraph 2) 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 Not applicable: this is an indexed combinatorial method, not a pretrained weight release. Individual claims | Strain level microbial detection and quantification with applications to single cell metagenomics Methods (paragraph 7); Discussion (paragraph 3) Version: version of record | inapplicable 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 reads and a reference-genome index Individual claims | Strain level microbial detection and quantification with applications to single cell metagenomics Results/Precision and recall in read classification across all species level queries (paragraph 2); Methods (paragraph 2) 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 Detected reference genomes and relative abundance estimates Individual claims | Strain level microbial detection and quantification with applications to single cell metagenomics Methods (paragraph 4); Results/Overview of CAMMiQ indexing and querying procedure (paragraph 2) 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 Not applicable: this is a reference-database algorithm rather than a neural model. Individual claims | Strain level microbial detection and quantification with applications to single cell metagenomics Results/Precision and recall in read classification across all species level queries (paragraph 3); Introduction (paragraph 3) Version: version of record | inapplicable 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 |
| Known versions / configuration CAMMiQ is the comparison-table label; that label does not specify an immutable weight revision. Individual claims | Strain level microbial detection and quantification with applications to single cell metagenomics Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. 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
- Strain level microbial detection and quantification with applications to single cell metagenomics · Original source · version of record
- algo-cancer/CAMMiQ README.md · Original source · 6142150d427a74cc21a5ee4d8b37a3b78884f163
- algo-cancer/CAMMiQ LICENSE · Original source · 6142150d427a74cc21a5ee4d8b37a3b78884f163
Technical metadata and extraction receipts
Stable ID: reported-model-32a19f43a4c254
- areas
- microbes-communities
- entity level
- method
- version
- Not reported
- reported name
- CAMMiQ
- 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: cammiq-2022; source locator: Methods (paragraph 3); Methods (paragraph 2) | Results/Overview of CAMMiQ indexing and querying procedure (paragraph 3); Methods (paragraph 2); 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.