ArticleInternational journal of molecular sciences2025
Pike: OTU-Level Analysis for Oxford Nanopore Amplicon Metagenomics.
Article in International journal of molecular sciences, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- Unraveling the Taxonomic Diversity and Functional Potential of the Tunisian Salterns, Abbassia and Thyna, via Integrated 16S-18S Amplicons and Shotgun Metagenomics.International journal of molecular sciences · 2026Article
- Pathogenic bacteria enriched in the oral microbiota might be associated with recurrent pulmonary infections in elderly individuals.Aging clinical and experimental research · 2025Article
- AI-powered analysis of viral metagenomic sequencing data for rapid outbreak investigation and novel pathogen discovery.Frontiers in microbiology · 2025Review
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Authors and funding
8 authors.
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Abstract
The Oxford Nanopore platform and nanopore sequencing are gaining increasing popularity in modern metagenomic research. However, there is a limited set of dedicated tools for analyzing this type of data. The tools used for nanopore amplicon sequencing data analysis often provide only taxonomy annotation without OTU sequence assembly. Conversely, tools that facilitate OTU assembly are constrained in their analysis to long reads, such as the V1-V9 regions of 16S rRNA for bacterial community studies or the full-length ITS cluster (ITS1-5.8S-ITS2) for fungal community studies. In other cases, researchers propose their own solutions without dedicated tools. In this paper, we present Pike, a novel tool for analyzing Oxford Nanopore amplicon sequencing data. Pike allows analysis without amplicon size limitations and allows de novo assembly of OTU sequences. In our research, we created mock communities of fungi and bacteria, which we then used to demonstrate the efficiency of our algorithm. Furthermore, we validated the algorithm using externally available data. We also compared our approach with similar ones to show its applicability.
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