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MetaMaps (Portik et al. 2022)

MetaMaps as run in Portik et al. 2022.

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MetaMaps as run in Portik et al. 2022.

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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-config-portik2022-metamaps-0-1-miniseq-h

areas: microbes-communities
contexts: clinical_research
method types: conventional_pipeline
reported name: MetaMaps
source locator: Table 2 row MetaMaps; Methods 'MetaMaps' and 'Reference databases' paragraph 4
foundation model eligible: false
version: 0.1
parameters: Pre-built MiniSeq + H database (12,058 complete RefSeq genomes); metamaps mapDirectly then classify

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: MetaMaps (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)	0.7 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 MetaMaps 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 'MetaMaps' (table row 10), column 'F0.5'
Configuration: MetaMaps (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)	0.78 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 MetaMaps 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 'MetaMaps' (table row 10), column 'F1'
Configuration: MetaMaps (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)	1 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 MetaMaps 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 'MetaMaps' (table row 10), column 'False negatives'
Configuration: MetaMaps (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)	10 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 MetaMaps 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 'MetaMaps' (table row 10), column 'False positives'
Configuration: MetaMaps (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)	53.1% 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 MetaMaps 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 'MetaMaps' (table row 10), column 'L1'
Configuration: MetaMaps (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)	0.66 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 MetaMaps 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 'MetaMaps' (table row 10), column 'Precision'
Configuration: MetaMaps (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)	0.95 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 MetaMaps 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 'MetaMaps' (table row 10), column 'Recall'
Configuration: MetaMaps (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)	19 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 MetaMaps 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 'MetaMaps' (table row 10), column 'True positives'
Configuration: MetaMaps (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)	0.21 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 MetaMaps 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 'MetaMaps*' (table row 31), column 'F0.5'
Configuration: MetaMaps (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)	0.29 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 MetaMaps 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 'MetaMaps*' (table row 31), column 'F1'
Configuration: MetaMaps (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)	4 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 MetaMaps 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 'MetaMaps*' (table row 31), column 'False negatives'
Configuration: MetaMaps (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)	50 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 MetaMaps 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 'MetaMaps*' (table row 31), column 'False positives'
Configuration: MetaMaps (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)	74.9% 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 MetaMaps 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 'MetaMaps*' (table row 31), column 'L1'
Configuration: MetaMaps (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)	0.18 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 MetaMaps 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 'MetaMaps*' (table row 31), column 'Precision'
Configuration: MetaMaps (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)	0.73 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 MetaMaps 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 'MetaMaps*' (table row 31), column 'Recall'
Configuration: MetaMaps (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)	11 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 MetaMaps 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 'MetaMaps*' (table row 31), column 'True positives'
Configuration: MetaMaps (Portik et al. 2022)	Protocol: ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION)	0.2 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 MetaMaps on ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION) dna-pathogen-20261009-protocol-portik2022-ont-q20-zymo-d6300-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'ONT Q20 Zymo D6300 (10 species, even)', row 'MetaMaps' (table row 59), column 'F0.5'
Configuration: MetaMaps (Portik et al. 2022)	Protocol: ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION)	0.28 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 MetaMaps on ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION) dna-pathogen-20261009-protocol-portik2022-ont-q20-zymo-d6300-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'ONT Q20 Zymo D6300 (10 species, even)', row 'MetaMaps' (table row 59), column 'F1'
Configuration: MetaMaps (Portik et al. 2022)	Protocol: ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION)	1 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 MetaMaps on ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION) dna-pathogen-20261009-protocol-portik2022-ont-q20-zymo-d6300-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'ONT Q20 Zymo D6300 (10 species, even)', row 'MetaMaps' (table row 59), column 'False negatives'
Configuration: MetaMaps (Portik et al. 2022)	Protocol: ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION)	45 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 MetaMaps on ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION) dna-pathogen-20261009-protocol-portik2022-ont-q20-zymo-d6300-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'ONT Q20 Zymo D6300 (10 species, even)', row 'MetaMaps' (table row 59), column 'False positives'
Configuration: MetaMaps (Portik et al. 2022)	Protocol: ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION)	14.2% 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 MetaMaps on ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION) dna-pathogen-20261009-protocol-portik2022-ont-q20-zymo-d6300-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'ONT Q20 Zymo D6300 (10 species, even)', row 'MetaMaps' (table row 59), column 'L1'
Configuration: MetaMaps (Portik et al. 2022)	Protocol: ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION)	0.17 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 MetaMaps on ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION) dna-pathogen-20261009-protocol-portik2022-ont-q20-zymo-d6300-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'ONT Q20 Zymo D6300 (10 species, even)', row 'MetaMaps' (table row 59), column 'Precision'
Configuration: MetaMaps (Portik et al. 2022)	Protocol: ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION)	0.9 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 MetaMaps on ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION) dna-pathogen-20261009-protocol-portik2022-ont-q20-zymo-d6300-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'ONT Q20 Zymo D6300 (10 species, even)', row 'MetaMaps' (table row 59), column 'Recall'
Configuration: MetaMaps (Portik et al. 2022)	Protocol: ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION)	9 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 MetaMaps on ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION) dna-pathogen-20261009-protocol-portik2022-ont-q20-zymo-d6300-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'ONT Q20 Zymo D6300 (10 species, even)', row 'MetaMaps' (table row 59), column 'True positives'
Configuration: MetaMaps (Portik et al. 2022)	Protocol: ONT R10.3 ZymoBIOMICS D6300 standard, length-filtered (GridION): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) Dataset: ONT R10.3 ZymoBIOMICS D6300 standard, length-filtered (GridION)	0.21 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 MetaMaps on ONT R10.3 ZymoBIOMICS D6300 standard, length-filtered (GridION) dna-pathogen-20261009-protocol-portik2022-ont-r10-zymo-d6300-species Aggregation: Not reported Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'ONT R10 Zymo D6300 (10 species, even)', row 'MetaMaps' (table row 45), column 'F0.5'