| Configuration: BugSeq-V2 (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 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 sourceBugSeq-V2 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 'BugSeq-V2' (table row 15), column 'F0.5' |
|---|
| Configuration: BugSeq-V2 (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) | 0.89 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBugSeq-V2 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 'BugSeq-V2' (table row 15), column 'F1' |
|---|
| Configuration: BugSeq-V2 (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) | 4 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 sourceBugSeq-V2 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 'BugSeq-V2' (table row 15), column 'False negatives' |
|---|
| Configuration: BugSeq-V2 (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-positive-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBugSeq-V2 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 'BugSeq-V2' (table row 15), column 'False positives' |
|---|
| Configuration: BugSeq-V2 (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) | 44.4% 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 sourceBugSeq-V2 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 'BugSeq-V2' (table row 15), column 'L1' |
|---|
| Configuration: BugSeq-V2 (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 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBugSeq-V2 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 'BugSeq-V2' (table row 15), column 'Precision' |
|---|
| Configuration: BugSeq-V2 (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) | 0.8 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBugSeq-V2 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 'BugSeq-V2' (table row 15), column 'Recall' |
|---|
| Configuration: BugSeq-V2 (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) | 16 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 sourceBugSeq-V2 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 'BugSeq-V2' (table row 15), column 'True positives' |
|---|
| Configuration: BugSeq-V2 (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) | 0.95 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 sourceBugSeq-V2 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 'BugSeq-V2*' (table row 36), column 'F0.5' |
|---|
| Configuration: BugSeq-V2 (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) | 0.89 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBugSeq-V2 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 'BugSeq-V2*' (table row 36), column 'F1' |
|---|
| Configuration: BugSeq-V2 (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 checkedMethods, coverage and sourceBugSeq-V2 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 'BugSeq-V2*' (table row 36), column 'False negatives' |
|---|
| Configuration: BugSeq-V2 (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 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 sourceBugSeq-V2 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 'BugSeq-V2*' (table row 36), column 'False positives' |
|---|
| Configuration: BugSeq-V2 (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) | 74.5% 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 sourceBugSeq-V2 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 'BugSeq-V2*' (table row 36), column 'L1' |
|---|
| Configuration: BugSeq-V2 (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 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBugSeq-V2 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 'BugSeq-V2*' (table row 36), column 'Precision' |
|---|
| Configuration: BugSeq-V2 (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 checkedMethods, coverage and sourceBugSeq-V2 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 'BugSeq-V2*' (table row 36), column 'Recall' |
|---|
| Configuration: BugSeq-V2 (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 checkedMethods, coverage and sourceBugSeq-V2 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 'BugSeq-V2*' (table row 36), column 'True positives' |
|---|
| Configuration: BugSeq-V2 (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) | 0.93 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 sourceBugSeq-V2 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 'BugSeq-V2' (table row 64), column 'F0.5' |
|---|
| Configuration: BugSeq-V2 (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) | 0.95 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBugSeq-V2 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 'BugSeq-V2' (table row 64), column 'F1' |
|---|
| Configuration: BugSeq-V2 (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 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 sourceBugSeq-V2 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 'BugSeq-V2' (table row 64), column 'False negatives' |
|---|
| Configuration: BugSeq-V2 (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-positive-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBugSeq-V2 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 'BugSeq-V2' (table row 64), column 'False positives' |
|---|
| Configuration: BugSeq-V2 (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) | 12.6% 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 sourceBugSeq-V2 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 'BugSeq-V2' (table row 64), column 'L1' |
|---|
| Configuration: BugSeq-V2 (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) | 0.91 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBugSeq-V2 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 'BugSeq-V2' (table row 64), column 'Precision' |
|---|
| Configuration: BugSeq-V2 (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 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBugSeq-V2 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 'BugSeq-V2' (table row 64), column 'Recall' |
|---|
| Configuration: BugSeq-V2 (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) | 10 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 sourceBugSeq-V2 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 'BugSeq-V2' (table row 64), column 'True positives' |
|---|
| Configuration: BugSeq-V2 (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) | 0.93 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 sourceBugSeq-V2 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 'BugSeq-V2' (table row 50), column 'F0.5' |
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