Evaluation

Sourmash-k31 on HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi)

Published DNA metagenomic classification comparison; transcribed, not reproduced.

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Evaluation results

1 evaluation · 8 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: Sourmash-k31 (Portik et al. 2022)	Protocol: HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi)	0.93 f-beta-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 on HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi) dna-pathogen-20261009-protocol-portik2022-hifi-zymo-d6331-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'HiFi Zymo D6331 (17 species, staggered)', row 'Sourmash-k31' (table row 29), column 'F0.5'
Configuration: Sourmash-k31 (Portik et al. 2022)	Protocol: HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi)	0.93 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 on HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi) dna-pathogen-20261009-protocol-portik2022-hifi-zymo-d6331-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'HiFi Zymo D6331 (17 species, staggered)', row 'Sourmash-k31' (table row 29), column 'F1'
Configuration: Sourmash-k31 (Portik et al. 2022)	Protocol: HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi)	1 false-negative-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 on HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi) dna-pathogen-20261009-protocol-portik2022-hifi-zymo-d6331-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'HiFi Zymo D6331 (17 species, staggered)', row 'Sourmash-k31' (table row 29), column 'False negatives'
Configuration: Sourmash-k31 (Portik et al. 2022)	Protocol: HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi)	1 false-positive-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 on HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi) dna-pathogen-20261009-protocol-portik2022-hifi-zymo-d6331-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'HiFi Zymo D6331 (17 species, staggered)', row 'Sourmash-k31' (table row 29), column 'False positives'
Configuration: Sourmash-k31 (Portik et al. 2022)	Protocol: HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi)	52% composition-l1-distance percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 on HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi) dna-pathogen-20261009-protocol-portik2022-hifi-zymo-d6331-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'HiFi Zymo D6331 (17 species, staggered)', row 'Sourmash-k31' (table row 29), column 'L1'
Configuration: Sourmash-k31 (Portik et al. 2022)	Protocol: HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi)	0.93 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 on HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi) dna-pathogen-20261009-protocol-portik2022-hifi-zymo-d6331-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'HiFi Zymo D6331 (17 species, staggered)', row 'Sourmash-k31' (table row 29), column 'Precision'
Configuration: Sourmash-k31 (Portik et al. 2022)	Protocol: HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi)	0.93 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 on HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi) dna-pathogen-20261009-protocol-portik2022-hifi-zymo-d6331-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'HiFi Zymo D6331 (17 species, staggered)', row 'Sourmash-k31' (table row 29), column 'Recall'
Configuration: Sourmash-k31 (Portik et al. 2022)	Protocol: HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi)	14 true-positive-count count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 on HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi) dna-pathogen-20261009-protocol-portik2022-hifi-zymo-d6331-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'HiFi Zymo D6331 (17 species, staggered)', row 'Sourmash-k31' (table row 29), column 'True positives'

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

Evaluation procedure

dna-pathogen-20261009-protocol-portik2022-hifi-zymo-d6331-species

Configuration: Sourmash-k31 (Portik et al. 2022)
Protocol: HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi): species detection at 0.001% of total reads (Portik et al. 2022 Table 4)
Dataset: HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi)

origin: Author-reported evaluation
configuration: Primary source as retrieved 2026-10-09
protocol id: dna-pathogen-20261009-protocol-portik2022-hifi-zymo-d6331-species
dataset version: NCBI SRX9569057
split: Single sequencing run
population: 15 scored species
inputs: HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi)
adaptation: None; reference databases as listed in Table 2
metric implementation: Authors' scoring of species read counts against the community composition
aggregation: Single dataset
budget: Not reported

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

Reproduction

Split: Single sequencing run
Adaptation: None; reference databases as listed in Table 2
Scoring implementation: Authors' scoring of species read counts against the community composition

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 None; reference databases as listed in Table 2 Context-only references	Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets Original source ↗ Table 4, dataset block 'HiFi Zymo D6331 (17 species, staggered)', row 'Sourmash-k31' (table row 29) Version: BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML Retrieved: 2026-10-09T19:45:04Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `42cf6834ec87e149752176a65247f3aab9873f7b215037a195175a8a3113c1fe` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.aggregation Single dataset Context-only references	Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets Original source ↗ Table 4, dataset block 'HiFi Zymo D6331 (17 species, staggered)', row 'Sourmash-k31' (table row 29) Version: BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML Retrieved: 2026-10-09T19:45:04Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `42cf6834ec87e149752176a65247f3aab9873f7b215037a195175a8a3113c1fe` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.budget Not reported Context-only references	Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets Original source ↗ Table 4, dataset block 'HiFi Zymo D6331 (17 species, staggered)', row 'Sourmash-k31' (table row 29) Version: BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML Retrieved: 2026-10-09T19:45:04Z	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `42cf6834ec87e149752176a65247f3aab9873f7b215037a195175a8a3113c1fe` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.dataset_version NCBI SRX9569057 Context-only references	Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets Original source ↗ Table 4, dataset block 'HiFi Zymo D6331 (17 species, staggered)', row 'Sourmash-k31' (table row 29) Version: BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML Retrieved: 2026-10-09T19:45:04Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `42cf6834ec87e149752176a65247f3aab9873f7b215037a195175a8a3113c1fe` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.inputs HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi) Context-only references	Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets Original source ↗ Table 4, dataset block 'HiFi Zymo D6331 (17 species, staggered)', row 'Sourmash-k31' (table row 29) Version: BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML Retrieved: 2026-10-09T19:45:04Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `42cf6834ec87e149752176a65247f3aab9873f7b215037a195175a8a3113c1fe` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.metric_implementation Authors' scoring of species read counts against the community composition Context-only references	Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets Original source ↗ Table 4, dataset block 'HiFi Zymo D6331 (17 species, staggered)', row 'Sourmash-k31' (table row 29) Version: BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML Retrieved: 2026-10-09T19:45:04Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.metric_implementation` Source artifact SHA-256: `42cf6834ec87e149752176a65247f3aab9873f7b215037a195175a8a3113c1fe` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.population 15 scored species Context-only references	Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets Original source ↗ Table 4, dataset block 'HiFi Zymo D6331 (17 species, staggered)', row 'Sourmash-k31' (table row 29) Version: BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML Retrieved: 2026-10-09T19:45:04Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.population` Source artifact SHA-256: `42cf6834ec87e149752176a65247f3aab9873f7b215037a195175a8a3113c1fe` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.protocol_id dna-pathogen-20261009-protocol-portik2022-hifi-zymo-d6331-species Context-only references	Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets Original source ↗ Table 4, dataset block 'HiFi Zymo D6331 (17 species, staggered)', row 'Sourmash-k31' (table row 29) Version: BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML Retrieved: 2026-10-09T19:45:04Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.protocol_id` Source artifact SHA-256: `42cf6834ec87e149752176a65247f3aab9873f7b215037a195175a8a3113c1fe` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.split Single sequencing run Context-only references	Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets Original source ↗ Table 4, dataset block 'HiFi Zymo D6331 (17 species, staggered)', row 'Sourmash-k31' (table row 29) Version: BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML Retrieved: 2026-10-09T19:45:04Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.split` Source artifact SHA-256: `42cf6834ec87e149752176a65247f3aab9873f7b215037a195175a8a3113c1fe` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.limitations 1 values Co-authors C. Titus Brown and N. Tessa Pierce-Ward are authors of the cited sourmash papers (references 33-35), so these rows are recorded as author_reported. Context-only references	Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets Original source ↗ Table 4, dataset block 'HiFi Zymo D6331 (17 species, staggered)', row 'Sourmash-k31' (table row 29) Version: BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML Retrieved: 2026-10-09T19:45:04Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.limitations` Source artifact SHA-256: `42cf6834ec87e149752176a65247f3aab9873f7b215037a195175a8a3113c1fe` 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

Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Original source · BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML

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Technical metadata and extraction receipts

Stable ID: dna-pathogen-20261009-eval-portik2022-hifi-zymo-d6331-sourmash-4-5-1-k31-genbank-2022-03

areas: microbes-communities
contexts: clinical_research
origin: author_reported
protocol: dna-pathogen-20261009-protocol-portik2022-hifi-zymo-d6331-species
version: Primary source as retrieved 2026-10-09
comparison: protocol id: dna-pathogen-20261009-protocol-portik2022-hifi-zymo-d6331-species; dataset version: NCBI SRX9569057; split: Single sequencing run; population: 15 scored species; inputs: HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi); adaptation: None; reference databases as listed in Table 2; metric implementation: Authors' scoring of species read counts against the community composition; aggregation: Single dataset; budget: Not reported
source locator: Table 4, dataset block 'HiFi Zymo D6331 (17 species, staggered)', row 'Sourmash-k31' (table row 29)
limitations: Co-authors C. Titus Brown and N. Tessa Pierce-Ward are authors of the cited sourmash papers (references 33-35), so these rows are recorded as author_reported.

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