Published DNA metagenomic classification comparison; transcribed, not reproduced.
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1 evaluation · 8 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Bracken (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) | 0.18 f-beta-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBracken 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 'Bracken' (table row 17), column 'F0.5' |
| Configuration: Bracken (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) | 0.26 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBracken 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 'Bracken' (table row 17), column 'F1' |
| Configuration: Bracken (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 checkedMethods, coverage and sourceBracken 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 'Bracken' (table row 17), column 'False negatives' |
| Configuration: Bracken (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) | 113 false-positive-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBracken 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 'Bracken' (table row 17), column 'False positives' |
| Configuration: Bracken (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) | 36.4% composition-l1-distance percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBracken 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 'Bracken' (table row 17), column 'L1' |
| Configuration: Bracken (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) | 0.15 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBracken 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 'Bracken' (table row 17), column 'Precision' |
| Configuration: Bracken (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 checkedMethods, coverage and sourceBracken 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 'Bracken' (table row 17), column 'Recall' |
| Configuration: Bracken (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 checkedMethods, coverage and sourceBracken 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 'Bracken' (table row 17), column 'True positives' |
Source checking is not independent reproduction. Release 2026-10-09-8cc1db47c7f9.
dna-pathogen-20261009-protocol-portik2022-illumina-atcc-msa1003-species
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18 evidence rows matching the loaded filters
| 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 Table 4, dataset block 'Illumina ATCC MSA1003 (20 species, staggered)', row 'Bracken' (table row 17) Version: BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.aggregation Single dataset Context-only references | 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 'Bracken' (table row 17) Version: BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.budget Not reported Context-only references | 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 'Bracken' (table row 17) Version: BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.dataset_version NCBI SRX5169925 Context-only references | 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 'Bracken' (table row 17) Version: BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.inputs Illumina ATCC MSA-1003 mock community (HiSeq 2500) Context-only references | 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 'Bracken' (table row 17) Version: BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| 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 Table 4, dataset block 'Illumina ATCC MSA1003 (20 species, staggered)', row 'Bracken' (table row 17) Version: BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.population 20 scored species Context-only references | 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 'Bracken' (table row 17) Version: BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.protocol_id dna-pathogen-20261009-protocol-portik2022-illumina-atcc-msa1003-species Context-only references | 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 'Bracken' (table row 17) Version: BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.split Single sequencing run Context-only references | 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 'Bracken' (table row 17) Version: BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.origin independent_paper Context-only references | 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 'Bracken' (table row 17) Version: BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-10-09-8cc1db47c7f9 · Record review: source checked
Stable ID: dna-pathogen-20261009-eval-portik2022-illumina-atcc-msa1003-bracken-2-6-0-pluspf