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Kraken2 (Portik et al. 2022)

Kraken2 as run in Portik et al. 2022.

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Kraken2 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-kraken2-2-1-1-pluspf

areas: microbes-communities
contexts: clinical_research
method types: conventional_pipeline
reported name: Kraken2
source locator: Table 2 row Kraken2; Methods 'Kraken2' and 'Reference databases' paragraph 2
foundation model eligible: false
version: 2.1.1
parameters: Database 'PlusPF' (pre-built, released 2021-01-27). Command: kraken2 --db PlusPF --threads 24 --report SAMPLE.kreport.txt SAMPLE.fasta

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Kraken2 (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)	0.21 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 Kraken2 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 'Kraken2' (table row 2), column 'F0.5'
Configuration: Kraken2 (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 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 Kraken2 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 'Kraken2' (table row 2), column 'F1'
Configuration: Kraken2 (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 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 Kraken2 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 'Kraken2' (table row 2), column 'False negatives'
Configuration: Kraken2 (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)	96 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 Kraken2 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 'Kraken2' (table row 2), column 'False positives'
Configuration: Kraken2 (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)	50.7% 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 Kraken2 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 'Kraken2' (table row 2), column 'L1'
Configuration: Kraken2 (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)	0.17 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 Kraken2 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 'Kraken2' (table row 2), column 'Precision'
Configuration: Kraken2 (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 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 Kraken2 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 'Kraken2' (table row 2), column 'Recall'
Configuration: Kraken2 (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)	20 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 Kraken2 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 'Kraken2' (table row 2), column 'True positives'
Configuration: Kraken2 (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)	0.08 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 Kraken2 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 'Kraken2*' (table row 23), column 'F0.5'
Configuration: Kraken2 (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)	0.13 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 Kraken2 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 'Kraken2*' (table row 23), column 'F1'
Configuration: Kraken2 (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	Independent external evaluation · Source checked Methods, coverage and source Kraken2 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 'Kraken2*' (table row 23), column 'False negatives'
Configuration: Kraken2 (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)	196 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 Kraken2 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 'Kraken2*' (table row 23), column 'False positives'
Configuration: Kraken2 (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)	51.9% 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 Kraken2 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 'Kraken2*' (table row 23), column 'L1'
Configuration: Kraken2 (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)	0.07 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 Kraken2 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 'Kraken2*' (table row 23), column 'Precision'
Configuration: Kraken2 (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	Independent external evaluation · Source checked Methods, coverage and source Kraken2 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 'Kraken2*' (table row 23), column 'Recall'
Configuration: Kraken2 (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	Independent external evaluation · Source checked Methods, coverage and source Kraken2 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 'Kraken2*' (table row 23), column 'True positives'
Configuration: Kraken2 (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)	0.24 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 Kraken2 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 'Kraken2' (table row 16), column 'F0.5'
Configuration: Kraken2 (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)	0.34 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 Kraken2 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 'Kraken2' (table row 16), column 'F1'
Configuration: Kraken2 (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 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 Kraken2 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 'Kraken2' (table row 16), column 'False negatives'
Configuration: Kraken2 (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)	77 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 Kraken2 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 'Kraken2' (table row 16), column 'False positives'
Configuration: Kraken2 (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)	44.8% 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 Kraken2 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 'Kraken2' (table row 16), column 'L1'
Configuration: Kraken2 (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)	0.21 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 Kraken2 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 'Kraken2' (table row 16), column 'Precision'
Configuration: Kraken2 (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 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 Kraken2 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 'Kraken2' (table row 16), column 'Recall'
Configuration: Kraken2 (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)	20 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 Kraken2 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 'Kraken2' (table row 16), column 'True positives'
Configuration: Kraken2 (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	0.17 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 Kraken2 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 'Kraken2' (table row 65), column 'F0.5'