Evaluation

minimap2 Myco on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)

Published DNA metagenomic classification comparison; transcribed, not reproduced.

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Evaluation results

1 evaluation · 5 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: minimap2 Myco (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)	11 peak-memory gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 Myco on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'minimap2 Myco', column 'Memory (GB)†'
Configuration: minimap2 Myco (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)	49,727 inference-throughput sample-per-second · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 Myco on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'minimap2 Myco', column 'Rate (reads/s)*'
Configuration: minimap2 Myco (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)	1 recall fraction · higher Uncertainty: 95% CI 0.9995 to 0.9996. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 Myco on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'minimap2 Myco', column 'Sensitivity (95% CI)'
Configuration: minimap2 Myco (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)	1 specificity fraction · higher Uncertainty: 95% CI 1.0 to 1.0. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 Myco on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'minimap2 Myco', column 'Specificity (95% CI)'
Configuration: minimap2 Myco (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)	1 youden-index fraction · higher Uncertainty: 95% CI 0.9994 to 0.9996. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 Myco on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'minimap2 Myco', column 'Youden’s index (95% CI)'

Source checking is not independent reproduction. Release 2026-10-09-8cc1db47c7f9.

Evaluation procedure

dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina

Configuration: minimap2 Myco (Hall and Coin 2024)
Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7)
Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)

origin: Author-reported evaluation
configuration: Primary source as retrieved 2026-10-09
protocol id: dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina
dataset version: ART v2016.06.05 MiSeq v3 150 bp paired reads at the same group proportions; 1,417,015 non-human read pairs (424 Mbp) classified
split: Single dataset
population: Non-human reads of the dataset
inputs: Non-human reads after the human read removal step
adaptation: Database as stated per configuration
metric implementation: Per-read confusion counts against known read origin
aggregation: All reads in the dataset
budget: 4 threads

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: Single dataset
Adaptation: Database as stated per configuration
Scoring implementation: Per-read confusion counts against known read origin

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

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Evidence table

Inspect claims, sources and review details

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19 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-09-8cc1db47c7f9
Property and statement	Original source and location	Review and provenance
attributes.comparison.adaptation Database as stated per configuration Context-only references	Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data Original source ↗ Table 7, row 'minimap2 Myco' Version: GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML Retrieved: 2026-10-09T19:55:15Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `ea3c34a01222d5c5203c52a85a700b7dae5cccd6f48e6d50808d5abbd6385554` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.aggregation All reads in the dataset Context-only references	Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data Original source ↗ Table 7, row 'minimap2 Myco' Version: GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML Retrieved: 2026-10-09T19:55:15Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `ea3c34a01222d5c5203c52a85a700b7dae5cccd6f48e6d50808d5abbd6385554` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.budget 4 threads Context-only references	Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data Original source ↗ Table 7, row 'minimap2 Myco' Version: GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML Retrieved: 2026-10-09T19:55:15Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `ea3c34a01222d5c5203c52a85a700b7dae5cccd6f48e6d50808d5abbd6385554` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.dataset_version ART v2016.06.05 MiSeq v3 150 bp paired reads at the same group proportions; 1,417,015 non-human read pairs (424 Mbp) classified Context-only references	Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data Original source ↗ Table 7, row 'minimap2 Myco' Version: GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML Retrieved: 2026-10-09T19:55:15Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `ea3c34a01222d5c5203c52a85a700b7dae5cccd6f48e6d50808d5abbd6385554` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.inputs Non-human reads after the human read removal step Context-only references	Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data Original source ↗ Table 7, row 'minimap2 Myco' Version: GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML Retrieved: 2026-10-09T19:55:15Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `ea3c34a01222d5c5203c52a85a700b7dae5cccd6f48e6d50808d5abbd6385554` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.metric_implementation Per-read confusion counts against known read origin Context-only references	Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data Original source ↗ Table 7, row 'minimap2 Myco' Version: GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML Retrieved: 2026-10-09T19:55:15Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.metric_implementation` Source artifact SHA-256: `ea3c34a01222d5c5203c52a85a700b7dae5cccd6f48e6d50808d5abbd6385554` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.population Non-human reads of the dataset Context-only references	Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data Original source ↗ Table 7, row 'minimap2 Myco' Version: GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML Retrieved: 2026-10-09T19:55:15Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.population` Source artifact SHA-256: `ea3c34a01222d5c5203c52a85a700b7dae5cccd6f48e6d50808d5abbd6385554` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.protocol_id dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Context-only references	Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data Original source ↗ Table 7, row 'minimap2 Myco' Version: GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML Retrieved: 2026-10-09T19:55:15Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.protocol_id` Source artifact SHA-256: `ea3c34a01222d5c5203c52a85a700b7dae5cccd6f48e6d50808d5abbd6385554` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.split Single dataset Context-only references	Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data Original source ↗ Table 7, row 'minimap2 Myco' Version: GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML Retrieved: 2026-10-09T19:55:15Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.split` Source artifact SHA-256: `ea3c34a01222d5c5203c52a85a700b7dae5cccd6f48e6d50808d5abbd6385554` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.limitations 1 values The database for this configuration was built or extended by the authors (Methods 'Mycobacterium read classification'). Context-only references	Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data Original source ↗ Table 7, row 'minimap2 Myco' Version: GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML Retrieved: 2026-10-09T19:55:15Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.limitations` Source artifact SHA-256: `ea3c34a01222d5c5203c52a85a700b7dae5cccd6f48e6d50808d5abbd6385554` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

Release 2026-10-09-8cc1db47c7f9 · Record review: source checked

1 source records and release history

Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Original source · GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML

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Technical metadata and extraction receipts

Stable ID: dna-pathogen-20261009-eval-hall2024-sim-illumina-minimap2-myco

areas: microbes-communities
contexts: clinical_research
origin: author_reported
protocol: dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina
version: Primary source as retrieved 2026-10-09
comparison: protocol id: dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina; dataset version: ART v2016.06.05 MiSeq v3 150 bp paired reads at the same group proportions; 1,417,015 non-human read pairs (424 Mbp) classified; split: Single dataset; population: Non-human reads of the dataset; inputs: Non-human reads after the human read removal step; adaptation: Database as stated per configuration; metric implementation: Per-read confusion counts against known read origin; aggregation: All reads in the dataset; budget: 4 threads
source locator: Table 7, row 'minimap2 Myco'
limitations: The database for this configuration was built or extended by the authors (Methods 'Mycobacterium read classification').

Related records

system: minimap2 Myco (Hall and Coin 2024)
assessment: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7)
data: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)
evaluation: hall2024-sim-illumina-minimap2-myco peak-memory
evaluation: hall2024-sim-illumina-minimap2-myco inference-throughput
evaluation: hall2024-sim-illumina-minimap2-myco recall (per read, M. tuberculosis)
evaluation: hall2024-sim-illumina-minimap2-myco specificity (per read, M. tuberculosis)
evaluation: hall2024-sim-illumina-minimap2-myco youden-index

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