ArticlemSystems
Application of a Database-Independent Approach To Assess the Quality of Operational Taxonomic Unit Picking Methods.
Article in mSystems. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
23 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The human gut pan-microbiome presents a compositional core formed by discrete phylogenetic units.Scientific reports · 2018Pooled it
- clustur: an R package for clustering features using sparse distance matrices.Microbiology resource announcements · 2025Article
- Isolation of Methane Enriched Bacterial Communities and Application as Wheat Biofertilizer under Drought Conditions: An Environmental Contribution.Plants (Basel, Switzerland) · 2023Article
- Best practice for wildlife gut microbiome research: A comprehensive review of methodology for 16S rRNA gene investigations.Frontiers in microbiology · 2023Review
- Effects of sulphur amino acids on the size and structure of microbial communities of aerobic granular sludge bioreactors.Amino acids · 2022Article
- Article
- Comparison of Methods for Picking the Operational Taxonomic Units From Amplicon Sequences.Frontiers in microbiology · 2021Article
- Role of Leaf Litter in Above-Ground Wood Decay.Microorganisms · 2020Article
- Reintroducing mothur: 10 Years Later.Applied and environmental microbiology · 2020Review
- Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods.Computational and structural biotechnology journal · 2020Review
- The Compositionally Distinct Cyanobacterial Biocrusts From Brazilian Savanna and Their Environmental Drivers of Community Diversity.Frontiers in microbiology · 2019Article
- Influence of salinity cycles in bioreactor performance and microbial community structure of membrane-based tidal-like variable salinity wastewater treatment systems.Environmental science and pollution research international · 2019Article
- DMSC: A Dynamic Multi-Seeds Method for Clustering 16S rRNA Sequences Into OTUs.Frontiers in microbiology · 2019Article
- Rapid analysis of metagenomic data using signature-based clustering.BMC bioinformatics · 2018Article
- HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies.Genome biology · 2018Article
- Microbial ecology of full-scale wastewater treatment systems in the Polar Arctic Circle: Archaea, Bacteria and Fungi.Scientific reports · 2018Article
- A comprehensive evaluation of the sl1p pipeline for 16S rRNA gene sequencing analysis.Microbiome · 2017Article
- Performing Skin Microbiome Research: A Method to the Madness.The Journal of investigative dermatology · 2017Review
- Diversity is the question, not the answer.The ISME journal · 2017Article
- Article
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1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Assignment of 16S rRNA gene sequences to operational taxonomic units (OTUs) allows microbial ecologists to overcome the inconsistencies and biases within bacterial taxonomy and provides a strategy for clustering similar sequences that do not have representatives in a reference database. I have applied the Matthews correlation coefficient to assess the ability of 15 reference-independent and -dependent clustering algorithms to assign sequences to OTUs. This metric quantifies the ability of an algorithm to reflect the relationships between sequences without the use of a reference and can be applied to any data set or method. The most consistently robust method was the average neighbor algorithm; however, for some data sets, other algorithms matched its performance.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.