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)

Presence or absence of each mock community species from the method's species-level read counts.

Overview

Presence or absence of each mock community species from the method's species-level read counts.

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14 recorded evaluations, 112 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Author-reported evaluations: 2
External evaluations: 12

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Sources and history

Release 2026-10-09-8cc1db47c7f9 · Record review: source checked

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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-protocol-portik2022-hifi-atcc-msa1003-species

areas: microbes-communities
contexts: clinical_research
protocol: A species is detected when its cumulative read count exceeds 0.001% of total reads (24 reads for this dataset). True positive: a mock community species detected; false positive: a detected species not in the community; false negative: a community species not detected. Precision, recall, F1 and F0.5 from these counts. L1: sum of absolute differences between estimated and theoretical species percent abundances, with all false positives pooled as 'Other' against a theoretical 0.
version: Table 4 block 'HiFi ATCC MSA1003'
source locator: Methods 'Detection metrics' paragraphs 1-4; 'Relative abundance estimates' paragraph 4; Table 3 (threshold read counts)
limitations: Mock community of cultured organisms; no human host DNA, no clinical specimen matrix.; Detection threshold is a fixed fraction of total reads, which penalises methods that assign fewer reads (Methods 'Detection metrics' paragraph 1).; Each method used its own reference database.
missing metadata: uncertainty: reason: unreported; note: Single run per dataset; no intervals printed

Related records

uses data: HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi)
part of: Mock community taxonomic profiling benchmark (Portik et al. 2022)
assessment: Bracken on HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi)
assessment: BugSeq-V2 on HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi)
assessment: Centrifuge-h22 on HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi)
assessment: Centrifuge-h500 on HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi)
assessment: Kraken2 on HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi)
assessment: MEGAN-LR-Nuc-HiFi on HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi)
assessment: MEGAN-LR-Nuc-ONT on HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi)
assessment: MEGAN-LR-Prot on HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi)
assessment: MetaMaps on HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi)
assessment: MetaPhlAn3 on HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi)
assessment: MMseqs2 on HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi)
assessment: mOTUs on HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi)
assessment: Sourmash-k31 on HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi)
assessment: Sourmash-k51 on HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi)
assessed by: Select a DNA pathogen-identification workflow for diagnostic testing

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