ArticlemSystems
Open-Source Sequence Clustering Methods Improve the State Of the Art.
Article in mSystems. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.
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85 citing papers in PubMed.
- Fecal microbiome and metabolome of infants fed bovine MFGM supplemented formula or standard formula with breast-fed infants as reference: a randomized controlled trial.Scientific reports · 2019Trial
- Microbial Transplantation With Human Gut Commensals Containing CutC Is Sufficient to Transmit Enhanced Platelet Reactivity and Thrombosis Potential.Circulation research · 2018Trial
- Comparative Effects of Exogenous Organic Amendments on Rhizosphere Microbial Communities and Soil Properties in Continuous Cropping Watermelon.Microorganisms · 2026Article
- Amplicon sequencing reveals the cryptic diversity in the dicyemid parasites of coleoid cephalopods sampled from the Atlantic and Pacific Oceans.Marine life science & technology · 2026Article
- A Comparative Analysis of DNA Metabarcoding and Morphological Identification in Diatoms Reveals Similar Patterns of Environmental Response.Ecology and evolution · 2026Article
- Review
- Microbial communities in the rhizosphere of tropical soils cultivated with maize as a function of nitrogen and phosphorus fertilizers.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2025Article
- Disease-resistant watermelon variety against Fusarium wilt by remodeling rhizosphere soil microenvironment.BMC microbiology · 2025Article
- Metatranscriptomic analysis reveals gut microbiome bacterial genes in pyruvate and amino acid metabolism associated with hyperuricemia and gout in humans.Scientific reports · 2025Article
- clustur: an R package for clustering features using sparse distance matrices.Microbiology resource announcements · 2025Article
- Maximizing Identification Precision of Hymenoptera and Brachycera (Diptera) With a Non-Destructive DNA Metabarcoding Approach.Ecology and evolution · 2025Article
- Insights into human respiratory microbiome under dysbiosis and its analysis tool.Frontiers in microbiomes · 2025Review
- Experimental evaluation of genetic variability based on DNA metabarcoding from the aquatic environment: Insights from the LerayEcology and evolution · 2024Article
- Population-based nanopore sequencing of the HIV-1 pangenome to identify drug resistance mutations.Scientific reports · 2024Article
- Analyzing microbial community and volatile compound profiles in the fermentation of cigar tobacco leaves.Applied microbiology and biotechnology · 2024Article
- Increased prokaryotic diversity in the Red Sea deep scattering layer.Environmental microbiome · 2023Article
- Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data.Scientific reports · 2023Article
- A Custom Regional DNA Barcode Reference Library for Lichen-Forming Fungi of the Intermountain West, USA, Increases Successful Specimen Identification.Journal of fungi (Basel, Switzerland) · 2023Article
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25 more citing papers are in PubMed but not listed here.
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10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sequence clustering is a common early step in amplicon-based microbial community analysis, when raw sequencing reads are clustered into operational taxonomic units (OTUs) to reduce the run time of subsequent analysis steps. Here, we evaluated the performance of recently released state-of-the-art open-source clustering software products, namely, OTUCLUST, Swarm, SUMACLUST, and SortMeRNA, against current principal options (UCLUST and USEARCH) in QIIME, hierarchical clustering methods in mothur, and USEARCH's most recent clustering algorithm, UPARSE. All the latest open-source tools showed promising results, reporting up to 60% fewer spurious OTUs than UCLUST, indicating that the underlying clustering algorithm can vastly reduce the number of these derived OTUs. Furthermore, we observed that stringent quality filtering, such as is done in UPARSE, can cause a significant underestimation of species abundance and diversity, leading to incorrect biological results. Swarm, SUMACLUST, and SortMeRNA have been included in the QIIME 1.9.0 release.
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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.