ArticlePeerJ2015
Swarm v2: highly-scalable and high-resolution amplicon clustering.
Article in PeerJ, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 192 papers.
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Who cites it
192 citing papers in PubMed.
- The Impact of Visible Symptoms of Thallus Damage on the Phycobiota of Mediterranean Epiphytic Lichens.Microbial ecology · 2026Article
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- Quantifying microbiota impact on plant traits for the guidance of breeding programs.The New phytologist · 2026Article
- Comparative Multi-Marker Environmental DNA Metabarcoding of Marine Metazoan Communities: Water vs. Sediment.Molecular ecology resources · 2026Article
- Metagenomic and biogenic amine changes in cassava fermentation for tucupi production using Pediococcus acidilactici starter culture.Journal of the science of food and agriculture · 2026Article
- Metabarcoding and targeted barcoding can enhance Norwegian Continental Shelf macrofauna species inventories.PeerJ · 2026Article
- Microbial communities associated with two populations of the spongeBiodiversity data journal · 2026Article
- Are Sponges Good Natural Sentinels for Monitoring Fish Diversity in Antarctic Coastal Waters?Ecology and evolution · 2025Article
- High-frequency sampling unveils biotic and abiotic drivers of rapid phytoplankton morphological changes.The New phytologist · 2025Article
- Broad Ecological Niche in Seashore Lichens Emerges From a Stable, Selective Association With Generalist Algal Symbionts.Ecology and evolution · 2025Article
- The diverse world within: age-dependent photobiont diversity in the lichen Protoparmeliopsis muralis.FEMS microbiology ecology · 2025Article
- Multi-Tool Marine Metabarcoding Bioassessment for Baselining and Monitoring Species and Communities in Kelp Habitats.Molecular ecology resources · 2025Article
- Freshwater Foraminifera Biodiversity in New England (USA): Evaluation of Field Sites and a Botanical Garden.Ecology and evolution · 2025Article
- A Long-Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS-MBON 2018-2020.Molecular ecology resources · 2025Article
- Plant Genetic Bases Associated With Microbiota Descriptors Shed Light Into a Novel Holobiont Generalist Genes Theory.Environmental microbiology · 2025Article
- Interest of inulin in obesity: comparison of the prebiotic effect of edible-food sources versus purified inulin from chicory root.European journal of nutrition · 2025Article
- Three-dimensional conservation planning of fish biodiversity metrics to achieve the deep-sea 30×30 conservation target.Conservation biology : the journal of the Society for Conservation Biology · 2025Article
- Metabarcoding identifies macroalgal composition as a driver of benthic invertebrate assemblages in restored habitats.Scientific reports · 2025Article
- Mangrove consortium resistant to the emerging contaminant DEHP: Composition, diversity, and ecological function of bacteria.PloS one · 2025Article
- Exploring microbial dynamics in ferruginous caves: taxonomic and functional diversity across seasons and cave zones.Frontiers in microbiology · 2025Article
132 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2, which has two important novel features: (1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and (2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks.
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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.