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Sourmash-k31 (Portik et al. 2022)

Sourmash-k31 as run in Portik et al. 2022.

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Sourmash-k31 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-sourmash-4-5-1-k31-genbank-2022-03

areas: microbes-communities
contexts: clinical_research
method types: conventional_pipeline
reported name: Sourmash-k31
source locator: Table 2 row sourmash (variation k31); Methods 'Sourmash' and 'Reference databases' paragraph 5
foundation model eligible: false
version: 4.5.1
parameters: GenBank 2022.03 pre-built databases (bacteria, archaea, viral, protozoa, fungi), scaled 1000, k = 31; sourmash gather then sourmash tax metagenome

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Sourmash-k31 (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)	0.83 f-beta-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 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 'Sourmash-k31' (table row 8), column 'F0.5'
Configuration: Sourmash-k31 (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	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 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 'Sourmash-k31' (table row 8), column 'F1'
Configuration: Sourmash-k31 (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	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 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 'Sourmash-k31' (table row 8), column 'False negatives'
Configuration: Sourmash-k31 (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)	5 false-positive-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 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 'Sourmash-k31' (table row 8), column 'False positives'
Configuration: Sourmash-k31 (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)	68.6% composition-l1-distance percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 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 'Sourmash-k31' (table row 8), column 'L1'
Configuration: Sourmash-k31 (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 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 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 'Sourmash-k31' (table row 8), column 'Precision'
Configuration: Sourmash-k31 (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	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 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 'Sourmash-k31' (table row 8), column 'Recall'
Configuration: Sourmash-k31 (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	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 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 'Sourmash-k31' (table row 8), column 'True positives'
Configuration: Sourmash-k31 (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 f-beta-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 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 'Sourmash-k31' (table row 29), column 'F0.5'
Configuration: Sourmash-k31 (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 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 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 'Sourmash-k31' (table row 29), column 'F1'
Configuration: Sourmash-k31 (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	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 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 'Sourmash-k31' (table row 29), column 'False negatives'
Configuration: Sourmash-k31 (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-positive-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 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 'Sourmash-k31' (table row 29), column 'False positives'
Configuration: Sourmash-k31 (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)	52% composition-l1-distance percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 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 'Sourmash-k31' (table row 29), column 'L1'
Configuration: Sourmash-k31 (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 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 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 'Sourmash-k31' (table row 29), column 'Precision'
Configuration: Sourmash-k31 (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	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 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 'Sourmash-k31' (table row 29), column 'Recall'
Configuration: Sourmash-k31 (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	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 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 'Sourmash-k31' (table row 29), column 'True positives'
Configuration: Sourmash-k31 (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)	0.78 f-beta-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 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 'Sourmash-k31' (table row 21), column 'F0.5'
Configuration: Sourmash-k31 (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)	0.85 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 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 'Sourmash-k31' (table row 21), column 'F1'
Configuration: Sourmash-k31 (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	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 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 'Sourmash-k31' (table row 21), column 'False negatives'
Configuration: Sourmash-k31 (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)	7 false-positive-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 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 'Sourmash-k31' (table row 21), column 'False positives'
Configuration: Sourmash-k31 (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)	57.2% composition-l1-distance percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 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 'Sourmash-k31' (table row 21), column 'L1'
Configuration: Sourmash-k31 (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)	0.74 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 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 'Sourmash-k31' (table row 21), column 'Precision'
Configuration: Sourmash-k31 (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	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 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 'Sourmash-k31' (table row 21), column 'Recall'
Configuration: Sourmash-k31 (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	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 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 'Sourmash-k31' (table row 21), column 'True positives'
Configuration: Sourmash-k31 (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	0.86 f-beta-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Sourmash-k31 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 'Sourmash-k31' (table row 70), column 'F0.5'