ArticleMicrobiome2022
LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis.
Article in Microbiome, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed.
- The Emerging Short Chain Fatty Acid Enriched Metabotype in Irritable Bowel Syndrome and Its Potential Clinical Relevance.Alimentary pharmacology & therapeutics · 2026Trial
- Modulating effects of microbiota on synbiotic intervention outcomes for microbiota-derived trimethylamine, trimethylamine N-oxide and indoxyl sulfate in healthy young medical students: insights from a 12-week randomized clinical trial.Journal of translational medicine · 2025Trial
- Systematic quantification and removal of host DNA contamination in 16S rRNA gene sequencing.Quantitative biology (Beijing, China) · 2026Article
- One species does not replace a community: functional roles of co-occurring translocated and endemic mycophagous mammals.Oecologia · 2026Article
- Land-Use Shapes Soil Fungal Communities and Functional Guilds in Tropical Forest Ecosystems.Plant-environment interactions (Hoboken, N.J.) · 2026Article
- Rewilding reshapes gut microbiomes and parasite exposure in European bison: a 17‑month release from Wilder Blean.Journal for nature conservation · 2026Article
- Gut Virome Characteristics and Network Alterations in IgA Nephropathy.Kidney international reports · 2026Article
- Response of Fungal Communities to Anthropogenic Disturbances in a Tropical Forest.Plant-environment interactions (Hoboken, N.J.) · 2026Article
- Article
- Soil management strategies shape bacterial and eukaryotic community structure in organic and inorganic systems of Malus × domestica production.Scientific reports · 2026Article
- LEMMIv2: benchmarking framework for metagenomic and 16S amplicon profilers with a catalogue of evaluated tools.Genome biology · 2026Article
- Copper is an intestinal habitat filter affecting the gut microbiota interactions with Salmonella Typhimurium.Microbiome · 2026Article
- Anxiety associated with dietary intake and gut microbiome features in a cross-sectional cohort of sub-clinically anxious young women.medRxiv : the preprint server for health sciences · 2026Article
- Microbial community assembly and pathogen signatures in groundwater and tap water systems in greater Cairo, Egypt.The Journal of the Egyptian Public Health Association · 2026Article
- Soil-Borne Pathogens Reflect Agricultural Land-Use Legacies.Ecology letters · 2026Article
- EasyAmplicon 2: Expanding PacBio and Nanopore Long Amplicon Sequencing Analysis Pipeline for Microbiome.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Response of mycorrhizal fungal communities to tree species composition and soil properties in the Miombo subtropical dry forest.Journal of biosciences · 2026Article
- Spatiotemporal dynamics of benthicFrontiers in microbiology · 2026Article
- Land Use Change Reshapes Climate-Driven Diversity Patterns of Tropical Arbuscular Mycorrhizal Fungi.Molecular ecology · 2026Article
- Arbuscular mycorrhizal associations persist in flooded sediment, with distinct communities in soil-borne and sediment-borne roots ofFrontiers in fungal biology · 2026Article
2 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
Abstract
backgroundAmplicon sequencing is an established and cost-efficient method for profiling microbiomes. However, many available tools to process this data require both bioinformatics skills and high computational power to process big datasets. Furthermore, there are only few tools that allow for long read amplicon data analysis. To bridge this gap, we developed the LotuS2 (less OTU scripts 2) pipeline, enabling user-friendly, resource friendly, and versatile analysis of raw amplicon sequences.
resultsIn LotuS2, six different sequence clustering algorithms as well as extensive pre- and post-processing options allow for flexible data analysis by both experts, where parameters can be fully adjusted, and novices, where defaults are provided for different scenarios. We benchmarked three independent gut and soil datasets, where LotuS2 was on average 29 times faster compared to other pipelines, yet could better reproduce the alpha- and beta-diversity of technical replicate samples. Further benchmarking a mock community with known taxon composition showed that, compared to the other pipelines, LotuS2 recovered a higher fraction of correctly identified taxa and a higher fraction of reads assigned to true taxa (48% and 57% at species; 83% and 98% at genus level, respectively). At ASV/OTU level, precision and F-score were highest for LotuS2, as was the fraction of correctly reported 16S sequences.
conclusionLotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. AVAILABILITY: LotuS2 is available from GitHub, conda, or via a Galaxy web interface, documented at http://lotus2.earlham.ac.uk/ . Video Abstract.
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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.