ArticleApplications in plant sciences
Balancing read length and sequencing depth: Optimizing Nanopore long-read sequencing for monocots with an emphasis on the Liliales.
Article in Applications in plant sciences. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- A Field-Deployable eDNA Metabarcoding Workflow Including De Novo Reference Assembly for Characterising Understudied Biodiversity Hotspots.Molecular ecology resources · 2026Article
- Article
- Benchmarking Illumina and Oxford Nanopore Technologies (ONT) sequencing platforms for whole genome sequencing of bacterial genomes and use in clinical microbiology.BMC medical genomics · 2026Article
- HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data.Nucleic acids research · 2026Article
- Rad51, Rad54, and ZMM proteins antagonize the mismatch repair system to promote fertility of budding yeast intraspecies hybrid zygotes.Nucleic acids research · 2025Article
- Comprehensive comparison of the third-generation sequencing tools for bacterial 6mA profiling.Nature communications · 2025Article
- Combination of Sample Preservation Approaches and DNA Extraction Methods for Long-Read Sequencing of Nudibranchs' Genomes.Ecology and evolution · 2025Article
- Evaluation of four DNA extraction kits for implementation of nanopore sequencing in routine surveillance of antimicrobial resistance in low-resource settings.Frontiers in microbiology · 2025Article
- A cry for kelp: Evidence for polyphenolic inhibition of Oxford Nanopore sequencing of brown algae.Journal of phycology · 2024Article
- Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection.Scientific reports · 2024Article
- Comparative evaluation of commercial DNA isolation approaches for nanopore-only bacterial genome assembly and plasmid recovery.Scientific reports · 2024Article
- Investigating the Quantification Capabilities of a Nanopore-Based Sequencing Platform for Food Safety Application via External Standards of Lambda DNA and Lambda Spiked Beef.Foods (Basel, Switzerland) · 2024Article
- Chromosomal evolution, environmental heterogeneity, and migration drive spatial patterns of species richness inProceedings of the National Academy of Sciences of the United States of America · 2024Article
- A targeted long-read sequencing approach questions the association of OXTR methylation with high-functioning autism.Clinical epigenetics · 2023Article
- What is the "modified" CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol.Applications in plant sciencesArticle
- Balancing read length and sequencing depth: Optimizing Nanopore long-read sequencing for monocots with an emphasis on the Liliales.Applications in plant sciencesArticle
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Premise: We present approaches used to generate long-read Nanopore sequencing reads for the Liliales and demonstrate how modifications to standard protocols directly impact read length and total output. The goal is to help those interested in generating long-read sequencing data determine which steps may be necessary for optimizing output and results. Methods: Four species of Results: Steps taken to maximize read length can decrease overall output. Notably, the number of pores in a flow cell is correlated with the overall output, yet we did not see an association between the pore number and the read length or the number of reads produced. Discussion: Many factors contribute to the overall success of a Nanopore sequencing run. We showed the direct impact that several modifications to the DNA extraction and cleaning steps have on the total sequencing output, read size, and number of reads generated. We show a tradeoff between read length and the number of reads and, to a lesser extent, the total sequencing output, all of which are important factors for successful de novo genome assembly.
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