rewirebio.iobenchmarks
Configuration

mOTUs (Portik et al. 2022)

mOTUs as run in Portik et al. 2022.

6 evaluations · 48 results

Overview

mOTUs as run in Portik et al. 2022.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

6 evaluations · 48 results. Different protocols are not a single leaderboard.

Filter evaluations

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: mOTUs (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

Independent external evaluation · Source checked
Methods, coverage and source

mOTUs 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 'mOTUs' (table row 7), column 'F0.5'
Configuration: mOTUs (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)
0.73 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

mOTUs 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 'mOTUs' (table row 7), column 'F1'
Configuration: mOTUs (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)
8 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

mOTUs 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 'mOTUs' (table row 7), column 'False negatives'
Configuration: mOTUs (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-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

mOTUs 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 'mOTUs' (table row 7), column 'False positives'
Configuration: mOTUs (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)
50.2% 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

mOTUs 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 'mOTUs' (table row 7), column 'L1'
Configuration: mOTUs (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)
0.92 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

mOTUs 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 'mOTUs' (table row 7), column 'Precision'
Configuration: mOTUs (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)
0.6 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

mOTUs 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 'mOTUs' (table row 7), column 'Recall'
Configuration: mOTUs (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)
12 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

mOTUs 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 'mOTUs' (table row 7), column 'True positives'
Configuration: mOTUs (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)
0.88 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

mOTUs 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 'mOTUs' (table row 28), column 'F0.5'
Configuration: mOTUs (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)
0.75 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

mOTUs 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 'mOTUs' (table row 28), column 'F1'
Configuration: mOTUs (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)
6 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

mOTUs 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 'mOTUs' (table row 28), column 'False negatives'
Configuration: mOTUs (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 checked
Methods, coverage and source

mOTUs 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 'mOTUs' (table row 28), column 'False positives'
Configuration: mOTUs (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)
63.6% 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

mOTUs 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 'mOTUs' (table row 28), column 'L1'
Configuration: mOTUs (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 checked
Methods, coverage and source

mOTUs 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 'mOTUs' (table row 28), column 'Precision'
Configuration: mOTUs (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)
0.6 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

mOTUs 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 'mOTUs' (table row 28), column 'Recall'
Configuration: mOTUs (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)
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

mOTUs 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 'mOTUs' (table row 28), column 'True positives'
Configuration: mOTUs (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)
0.5 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

mOTUs 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 'mOTUs' (table row 20), column 'F0.5'
Configuration: mOTUs (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)
0.32 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

mOTUs 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 'mOTUs' (table row 20), column 'F1'
Configuration: mOTUs (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)
16 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

mOTUs 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 'mOTUs' (table row 20), column 'False negatives'
Configuration: mOTUs (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 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

mOTUs 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 'mOTUs' (table row 20), column 'False positives'
Configuration: mOTUs (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)
51.6% 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

mOTUs 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 'mOTUs' (table row 20), column 'L1'
Configuration: mOTUs (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)
0.8 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

mOTUs 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 'mOTUs' (table row 20), column 'Precision'
Configuration: mOTUs (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)
0.2 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

mOTUs 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 'mOTUs' (table row 20), column 'Recall'
Configuration: mOTUs (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)
4 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

mOTUs 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 'mOTUs' (table row 20), column 'True positives'
Configuration: mOTUs (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
0.92 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

mOTUs 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 'mOTUs' (table row 69), column 'F0.5'

Source checking is not independent reproduction. Release 2026-10-09-8cc1db47c7f9.

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Evidence

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Evidence table

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Claims, original sources and review scope · Release 2026-10-09-8cc1db47c7f9
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Release 2026-10-09-8cc1db47c7f9 · Record review: source checked

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Technical metadata and extraction receipts

Stable ID: dna-pathogen-20261009-config-portik2022-motus2-3-0-3

areas
microbes-communities
contexts
clinical_research
method types
conventional_pipeline
reported name
mOTUs
source locator
Table 2 row mOTUs2; Methods 'mOTUs2' and 'Reference databases' paragraph 3
foundation model eligible
false
version
mOTUs2 v3.0.3 (database version 3.0.3)
parameters
Long reads converted with motus prep_long, then motus profile -c
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