Configuration

MetaPhlAn3 (Portik et al. 2022)

MetaPhlAn3 as run in Portik et al. 2022.

Overview

MetaPhlAn3 as run in Portik et al. 2022.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

6 evaluations · 48 results. Different protocols are not a single leaderboard.

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

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

Use this model

How it works, versions and access

Strengths, limitations and unresolved questions

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

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.

0 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

No evidence rows match these filters. Choose another scope or clear the search.

All evidence (JSONL) (gzip)How to read the evidence

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

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: dna-pathogen-20261009-config-portik2022-metaphlan-3-0-7-mpa-v30-201901

areas: microbes-communities
contexts: clinical_research
method types: conventional_pipeline
reported name: MetaPhlAn3
source locator: Table 2 row MetaPhlAn3; Methods 'MetaPhlAn3'
foundation model eligible: false
version: 3.0.7
parameters: Database mpa_v30_CHOCOPhlAn_201901; alignments made externally with bowtie2 --local, then metaphlan --input_type sam

Related records

Suggest a correction

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: MetaPhlAn3 (Portik et al. 2022)	Protocol: HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi)	0.29 f-beta-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MetaPhlAn3 on HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi) dna-pathogen-20261009-protocol-portik2022-hifi-atcc-msa1003-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'HiFi ATCC MSA1003', row 'MetaPhlAn3' (table row 6), column 'F0.5'
Configuration: MetaPhlAn3 (Portik et al. 2022)	Protocol: HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi)	0.37 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MetaPhlAn3 on HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi) dna-pathogen-20261009-protocol-portik2022-hifi-atcc-msa1003-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'HiFi ATCC MSA1003', row 'MetaPhlAn3' (table row 6), column 'F1'
Configuration: MetaPhlAn3 (Portik et al. 2022)	Protocol: HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi)	7 false-negative-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MetaPhlAn3 on HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi) dna-pathogen-20261009-protocol-portik2022-hifi-atcc-msa1003-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'HiFi ATCC MSA1003', row 'MetaPhlAn3' (table row 6), column 'False negatives'
Configuration: MetaPhlAn3 (Portik et al. 2022)	Protocol: HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi)	38 false-positive-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MetaPhlAn3 on HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi) dna-pathogen-20261009-protocol-portik2022-hifi-atcc-msa1003-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'HiFi ATCC MSA1003', row 'MetaPhlAn3' (table row 6), column 'False positives'
Configuration: MetaPhlAn3 (Portik et al. 2022)	Protocol: HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi)	45.2% composition-l1-distance percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MetaPhlAn3 on HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi) dna-pathogen-20261009-protocol-portik2022-hifi-atcc-msa1003-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'HiFi ATCC MSA1003', row 'MetaPhlAn3' (table row 6), column 'L1'
Configuration: MetaPhlAn3 (Portik et al. 2022)	Protocol: HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi)	0.26 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MetaPhlAn3 on HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi) dna-pathogen-20261009-protocol-portik2022-hifi-atcc-msa1003-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'HiFi ATCC MSA1003', row 'MetaPhlAn3' (table row 6), column 'Precision'
Configuration: MetaPhlAn3 (Portik et al. 2022)	Protocol: HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi)	0.65 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MetaPhlAn3 on HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi) dna-pathogen-20261009-protocol-portik2022-hifi-atcc-msa1003-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'HiFi ATCC MSA1003', row 'MetaPhlAn3' (table row 6), column 'Recall'
Configuration: MetaPhlAn3 (Portik et al. 2022)	Protocol: HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi)	13 true-positive-count count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MetaPhlAn3 on HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi) dna-pathogen-20261009-protocol-portik2022-hifi-atcc-msa1003-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'HiFi ATCC MSA1003', row 'MetaPhlAn3' (table row 6), column 'True positives'
Configuration: MetaPhlAn3 (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)	0.4 f-beta-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MetaPhlAn3 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 'MetaPhlAn3*' (table row 27), column 'F0.5'
Configuration: MetaPhlAn3 (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)	0.49 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MetaPhlAn3 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 'MetaPhlAn3*' (table row 27), column 'F1'
Configuration: MetaPhlAn3 (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)	3 false-negative-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MetaPhlAn3 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 'MetaPhlAn3*' (table row 27), column 'False negatives'
Configuration: MetaPhlAn3 (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)	22 false-positive-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MetaPhlAn3 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 'MetaPhlAn3*' (table row 27), column 'False positives'
Configuration: MetaPhlAn3 (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)	53.8% composition-l1-distance percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MetaPhlAn3 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 'MetaPhlAn3*' (table row 27), column 'L1'
Configuration: MetaPhlAn3 (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)	0.35 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MetaPhlAn3 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 'MetaPhlAn3*' (table row 27), column 'Precision'
Configuration: MetaPhlAn3 (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)	0.8 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MetaPhlAn3 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 'MetaPhlAn3*' (table row 27), column 'Recall'
Configuration: MetaPhlAn3 (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)	12 true-positive-count count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MetaPhlAn3 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 'MetaPhlAn3*' (table row 27), column 'True positives'
Configuration: MetaPhlAn3 (Portik et al. 2022)	Protocol: Illumina ATCC MSA-1003 mock community (HiSeq 2500): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: Illumina ATCC MSA-1003 mock community (HiSeq 2500)	0.83 f-beta-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MetaPhlAn3 on Illumina ATCC MSA-1003 mock community (HiSeq 2500) dna-pathogen-20261009-protocol-portik2022-illumina-atcc-msa1003-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'Illumina ATCC MSA1003 (20 species, staggered)', row 'MetaPhlAn3' (table row 19), column 'F0.5'
Configuration: MetaPhlAn3 (Portik et al. 2022)	Protocol: Illumina ATCC MSA-1003 mock community (HiSeq 2500): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: Illumina ATCC MSA-1003 mock community (HiSeq 2500)	0.73 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MetaPhlAn3 on Illumina ATCC MSA-1003 mock community (HiSeq 2500) dna-pathogen-20261009-protocol-portik2022-illumina-atcc-msa1003-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'Illumina ATCC MSA1003 (20 species, staggered)', row 'MetaPhlAn3' (table row 19), column 'F1'
Configuration: MetaPhlAn3 (Portik et al. 2022)	Protocol: Illumina ATCC MSA-1003 mock community (HiSeq 2500): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: Illumina ATCC MSA-1003 mock community (HiSeq 2500)	8 false-negative-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MetaPhlAn3 on Illumina ATCC MSA-1003 mock community (HiSeq 2500) dna-pathogen-20261009-protocol-portik2022-illumina-atcc-msa1003-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'Illumina ATCC MSA1003 (20 species, staggered)', row 'MetaPhlAn3' (table row 19), column 'False negatives'
Configuration: MetaPhlAn3 (Portik et al. 2022)	Protocol: Illumina ATCC MSA-1003 mock community (HiSeq 2500): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: Illumina ATCC MSA-1003 mock community (HiSeq 2500)	1 false-positive-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MetaPhlAn3 on Illumina ATCC MSA-1003 mock community (HiSeq 2500) dna-pathogen-20261009-protocol-portik2022-illumina-atcc-msa1003-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'Illumina ATCC MSA1003 (20 species, staggered)', row 'MetaPhlAn3' (table row 19), column 'False positives'
Configuration: MetaPhlAn3 (Portik et al. 2022)	Protocol: Illumina ATCC MSA-1003 mock community (HiSeq 2500): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: Illumina ATCC MSA-1003 mock community (HiSeq 2500)	12.7% composition-l1-distance percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MetaPhlAn3 on Illumina ATCC MSA-1003 mock community (HiSeq 2500) dna-pathogen-20261009-protocol-portik2022-illumina-atcc-msa1003-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'Illumina ATCC MSA1003 (20 species, staggered)', row 'MetaPhlAn3' (table row 19), column 'L1'
Configuration: MetaPhlAn3 (Portik et al. 2022)	Protocol: Illumina ATCC MSA-1003 mock community (HiSeq 2500): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: Illumina ATCC MSA-1003 mock community (HiSeq 2500)	0.92 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MetaPhlAn3 on Illumina ATCC MSA-1003 mock community (HiSeq 2500) dna-pathogen-20261009-protocol-portik2022-illumina-atcc-msa1003-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'Illumina ATCC MSA1003 (20 species, staggered)', row 'MetaPhlAn3' (table row 19), column 'Precision'
Configuration: MetaPhlAn3 (Portik et al. 2022)	Protocol: Illumina ATCC MSA-1003 mock community (HiSeq 2500): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: Illumina ATCC MSA-1003 mock community (HiSeq 2500)	0.6 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MetaPhlAn3 on Illumina ATCC MSA-1003 mock community (HiSeq 2500) dna-pathogen-20261009-protocol-portik2022-illumina-atcc-msa1003-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'Illumina ATCC MSA1003 (20 species, staggered)', row 'MetaPhlAn3' (table row 19), column 'Recall'
Configuration: MetaPhlAn3 (Portik et al. 2022)	Protocol: Illumina ATCC MSA-1003 mock community (HiSeq 2500): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: Illumina ATCC MSA-1003 mock community (HiSeq 2500)	12 true-positive-count count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MetaPhlAn3 on Illumina ATCC MSA-1003 mock community (HiSeq 2500) dna-pathogen-20261009-protocol-portik2022-illumina-atcc-msa1003-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'Illumina ATCC MSA1003 (20 species, staggered)', row 'MetaPhlAn3' (table row 19), column 'True positives'
Configuration: MetaPhlAn3 (Portik et al. 2022)	Protocol: Illumina ZymoBIOMICS D6300 standard (NovaSeq 6000), subsampled: species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: Illumina ZymoBIOMICS D6300 standard (NovaSeq 6000), subsampled	0.83 f-beta-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MetaPhlAn3 on Illumina ZymoBIOMICS D6300 standard (NovaSeq 6000), subsampled dna-pathogen-20261009-protocol-portik2022-illumina-zymo-d6300-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'Illumina Zymo D6300 (10 species, even)', row 'MetaPhlAn3' (table row 68), column 'F0.5'