ArticleBMC genomics2025
Biases from Oxford Nanopore library preparation kits and their effects on microbiome and genome analysis.
Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
14 citing papers in PubMed.
- Review
- Amplification-Free Nanopore Sequencing for Herpesvirus DNA Detection in Intraocular Fluids.Ophthalmology science · 2026Article
- Growth Phase-Related DNA Methylation and Localized DNA Fragment Density Variation inEpigenomes · 2026Article
- Applicability of Nanopore-only whole-genome sequencing forJournal of clinical microbiology · 2026Article
- Barbell reveals and resolves demultiplexing and trimming issues in Nanopore data.Bioinformatics (Oxford, England) · 2026Article
- How to Unmask an Unknown: The Restriction-Modification SystemInternational journal of molecular sciences · 2026Article
- esloco: simulation-based estimation of local coverage in long-read DNA sequencing.Bioinformatics (Oxford, England) · 2026Article
- Genomic characterisation of extensively drug-resistant Acinetobacter baumannii isolates from a tertiary hospital in Ghana.PloS one · 2026Article
- Optimization of nanopore sequencing for surveillance of antimicrobial resistance in low-resource settings.Frontiers in public health · 2026Article
- Development of high-throughput analytical methods for characterization and quantitation of rAAV genome integrity.Molecular therapy. Methods & clinical development · 2025Article
- Towards the integration of antibiotic resistance gene mobility into environmental surveillance and risk assessment.npj antimicrobials and resistance · 2025Review
- Understanding prokaryotic adaptation through advanced DNA methylation detection techniques.The ISME journal · 2025Review
- Decoding microbiome responses to quarantine potato wart disease: first insights into suppression and biocontrol by full-length 16S rRNA gene profiling and functional prediction.Frontiers in plant science · 2025Article
- Multiomics Research: Principles and Challenges in Integrated Analysis.Biodesign research · 2024Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
backgroundOxford Nanopore sequencing is a long-read sequencing technology that does not rely on a polymerase to generate sequence data. Sequencing library preparation methods used in Oxford Nanopore sequencing rely on the addition of a motor protein bound to an adapter sequence, which is added either using ligation-based methods (ligation sequencing kit), or transposase-based methods (rapid sequencing kit). However, these methods have enzymatic steps that may be susceptible to motif bias, including the underrepresentation of adenine-thymine (AT) sequences due to ligation and biases from transposases. This study aimed to compare the recognition motif and relative interaction frequencies of these library preparation methods and assess their effects on relative sequencing coverage, microbiome, and methylation profiles. The impacts of DNA extraction kits and basecalling models on microbiome analysis were also investigated.
resultsBy using sequencing data generated by the ligation and rapid library kits, we identified the recognition motif (5'-TATGA-3') consistent with MuA transposase in the rapid kit and low frequencies of AT in the sequence terminus of the ligation kit. The rapid kit showed reduced yield in regions with 40-70% guanine-cytosine (GC) contents, while the ligation kit showed relatively even coverage distribution in areas with various GC contents. Due to longer reads, ligation kits showed increased taxonomic classification efficiency compared to the rapid protocols. Rumen microbial profile at different taxonomic levels and mock community profile showed significant variation due to the library preparation method used. The ligation kit outperformed the rapid kit in subsequent bacterial DNA methylation statistics, although there were no significant differences.
conclusionsOur findings indicated that careful and consistent library preparation method selection is essential for quantitative methods such as bovine-related microbiome analysis due to the systematic bias induced by the enzymatic reactions in Oxford Nanopore library preparation.
Indexed as
Identifiers
What OpenQuestion holds
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.