ArticleMolecular ecology resources2022
High molecular weight DNA extraction strategies for long-read sequencing of complex metagenomes.
Article in Molecular ecology resources, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 51 citations in OpenAlex.
- Pan-genomics and multi-omics for deciphering genetic variation and accelerating genetic improvement in ruminant livestock.Functional & integrative genomics · 2026Review
- Toward the clinical application of long-read sequencing in repeat-expansion disorders.Nature genetics · 2026Review
- Long-read sequencing for neurological disorders: opportunities, challenges, and future directions.Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology · 2026Review
- Long-Read Sequencing in CKD Diagnostics: Breaking Genomic Barriers and Expanding Global Inclusion.Kidney international reports · 2026Review
- Performance of mechanically sheared DNA in multiplexed Oxford Nanopore sequencing forMicrobial genomics · 2026Article
- Assessment of DNA Variations From Two In Vivo Skeletal Muscle Disorder Mouse Models Using Complementary Square-Wave Voltammetry and LC-MS/MS Analysis.Chembiochem : a European journal of chemical biology · 2026Article
- Article
- Comparative Profiling of Yeast Communities in Kefir Grains and Liquid Kefir Using ITS Amplicon Next-Generation Sequencing.International journal of food science · 2026Article
- Sample Preparation for Multi-Omics Analysis: Considerations and Guidance for Identifying the Ideal Workflow.Proteomics · 2025Review
- Rapid Nanopore Sequencing of Positive Blood Cultures Using Automated Benzyl-Alcohol Extraction Improves Time-Critical Sepsis Management.Antibiotics (Basel, Switzerland) · 2025Article
- Unveiling the potential of bioslurry and biogenic ZnO nanoparticles formulation as significant bionanofertilizer by ameliorating rhizospheric microbiome of Vigna radiata.International microbiology : the official journal of the Spanish Society for Microbiology · 2025Article
- Ultra pure high molecular weight DNA from soil for Nanopore shotgun metagenomics and metabarcoding sequencing.MethodsX · 2025Article
- Long-Read Sequencing: The Third Generation of Diagnostic Testing for Dystonia.Movement disorders : official journal of the Movement Disorder Society · 2025Review
- Metaproteomic Profiling of the Secretome of a Granule-forming Ca. Accumulibacter Enrichment.Proteomics · 2025Article
- Combination of Sample Preservation Approaches and DNA Extraction Methods for Long-Read Sequencing of Nudibranchs' Genomes.Ecology and evolution · 2025Article
- Long-Read Sequencing for the Rapid Response to Infectious Diseases Outbreaks.Current clinical microbiology reports · 2025Review
- Nanopore sequencing in veterinary medicine: from concepts to clinical applications.Frontiers in cellular and infection microbiology · 2025Review
- Essential nucleic acid omics: a theoretical foundation for early-stage users.Frontiers in bioinformatics · 2025Review
- A Step-by-Step Guide to Sequencing and Assembly of Complete Bacterial Genomes Using the Oxford Nanopore MinION.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Evaluation of Commercial RNA Extraction Protocols for Avian Influenza Virus Using Nanopore Metagenomic Sequencing.Viruses · 2024Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
By offering extremely long contiguous characterization of individual DNA molecules, rapidly emerging long-read sequencing strategies offer comprehensive insights into the organization of genetic information in genomes and metagenomes. However, successful long-read sequencing experiments demand high concentrations of highly purified DNA of high molecular weight (HMW), which limits the utility of established DNA extraction kits designed for short-read sequencing. The challenges associated with input DNA quality intensify further when working with complex environmental samples of low microbial biomass, which requires new protocols that are tailored to study metagenomes with long-read sequencing. Here, we use human tongue scrapings to benchmark six HMW DNA extraction strategies that are based on commercially available kits, phenol-chloroform (PC) extraction and agarose encasement followed by agarase digestion. A typical end goal of HMW DNA extractions is to obtain the longest possible reads during sequencing, which is often achieved by PC extractions, as demonstrated in sequencing of cultured cells. Yet our analyses that consider overall read-size distribution, assembly performance and the number of circularized elements found in sequencing results suggest that column-based kits with enzyme supplementation, rather than PC methods, may be more appropriate for long-read sequencing of metagenomes.
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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.