benchmark · task

Strain-level abundance quantification

This paper-specific evaluation tests Strain-level abundance quantification using HumanGut-all strain-level query.

At a glance

Explanatory profile: limited source coverage · Automated source review, 2026-09-16. This does not change the review status of its results.

Data, procedure and scoring
Property	Description and evidence
Record type	Paper-specific task; protocol incompletely extractedStrain level microbial detection and quantification with applications to single cell metagenomics · Table 5, B. L1 Err. / HumanGut-all row, CAMMiQ L1 Err. column; Table 5, B. L1 Err. / HumanGut-all row, Kraken2 L1 Err. column
Inputs	HumanGut-all strain-level queryStrain level microbial detection and quantification with applications to single cell metagenomics · Table 5, B. L1 Err. / HumanGut-all row, CAMMiQ L1 Err. column; Table 5, B. L1 Err. / HumanGut-all row, Kraken2 L1 Err. column
Assessment	L1 abundance errorStrain level microbial detection and quantification with applications to single cell metagenomics · Table 5, B. L1 Err. / HumanGut-all row, CAMMiQ L1 Err. column; Table 5, B. L1 Err. / HumanGut-all row, Kraken2 L1 Err. column
Recorded split or evaluation setting	UnextractedStrain level microbial detection and quantification with applications to single cell metagenomics · Table 5, B. L1 Err. / HumanGut-all row, CAMMiQ L1 Err. column; Table 5, B. L1 Err. / HumanGut-all row, Kraken2 L1 Err. column
Datasets	Not extracted or verified for this record.
Organisms	Not extracted or verified for this record.
Assays	Not extracted or verified for this record.
Adaptation	Not extracted or verified for this record.
Baselines	Not extracted or verified for this record.

How it works

Reported evaluation outline

Outline of the existing paper extraction. Split membership, fitting details and scorer implementation remain incompletely reviewed.

Read the diagram as text

HumanGut-all strain-level query
Recorded fitting or scoring procedure
Assess L1 abundance error

Strain level microbial detection and quantification with applications to single cell metagenomics · Table 5, B. L1 Err. / HumanGut-all row, CAMMiQ L1 Err. column; Table 5, B. L1 Err. / HumanGut-all row, Kraken2 L1 Err. column

Evaluation context

The existing paper extraction describes: Strain-level quantification on the HumanGut-all synthetic query. This description is retained with the exact evaluation records; it is not a new protocol reconstruction.

Tested models and results

Release 2026-09-16-d74d282221a9 · 2 evaluations · 2 metric rows. Different protocols are not a single leaderboard.

Evaluated configurationMetricEvidence origin

Results grouped by the exact reported evaluation
Metric and finding	Coverage and uncertainty	Evidence
CAMMiQ: Strain-level abundance quantification Model: CAMMiQ · Benchmark: Strain-level abundance quantification · Dataset: 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 Model: Kraken2 · Benchmark: Strain-level abundance quantification · Dataset: 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.

Strengths and limitations

Strengths and considerations

The linked evaluation identifies the paper-specific dataset and assessment rather than treating the task name as a universal benchmark.Strain level microbial detection and quantification with applications to single cell metagenomics · Table 5, B. L1 Err. / HumanGut-all row, CAMMiQ L1 Err. column; Table 5, B. L1 Err. / HumanGut-all row, Kraken2 L1 Err. column

Limitations and conditions

The numerical table check does not establish the full data-processing, fitting or leakage-control protocol.Strain level microbial detection and quantification with applications to single cell metagenomics · Table 5, B. L1 Err. / HumanGut-all row, CAMMiQ L1 Err. column; Table 5, B. L1 Err. / HumanGut-all row, Kraken2 L1 Err. column

Profile review details

Catalogue extraction inspected; protocol claims remain limited to the cited evidence. Missing details are not presumed absent from the original paper.

Stable record: reported-task-571f0a2e7faed3

Sources and history

Release 2026-09-16-d74d282221a9 · Record review: needs review

Strain level microbial detection and quantification with applications to single cell metagenomics · Original source · version of record

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Technical metadata and extraction receipts

Stable ID: reported-task-571f0a2e7faed3

areas: microbes-communities
tasks: Strain-level abundance quantification
entity level: task
version: Not reported
task: Strain-level abundance quantification
scope note: Paper-specific evaluation task; protocol completeness requires further extraction.
missing metadata: protocol version: not_reported_in_legacy_extract; split: not_reported_in_legacy_extract

Related records

dataset: HumanGut-all strain-level query
benchmark: CAMMiQ: Strain-level abundance quantification
benchmark: Kraken2: Strain-level abundance quantification

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