Evidence map›Paper›PMID 39546195›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2025

A Step-by-Step Guide to Sequencing and Assembly of Complete Bacterial Genomes Using the Oxford Nanopore MinION.

Anil Kumar, Max M Häggblom, Lee J Kerkhof

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Review
  2. Article
  3. Nanopore sequencing in veterinary medicine: from concepts to clinical applications.Frontiers in cellular and infection microbiology · 2025
    Review
  4. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Anil KumarDepartment of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA.
Max M HäggblomDepartment of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA.
Lee J KerkhofDepartment of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA. lkerkhof@rutgers.edu.

Funding

USDA National Institute of Food and Agriculture 1012785U.S. National Science Foundation 2129351
6 · The paper itself

Abstract

The Oxford Nanopore (ONT) MinION enables sequencing of longer DNA/RNA fragments compared to other sequencers, such as Illumina, etc. This nanopore method provides distinct advantages for generating complete genome assemblies from microorganisms. Specifically, the R9.4 flow cells used for MinION sequencing have much lower error rates compared with earlier versions of the ONT platform. Coupled with base calling using Dorado software, higher-quality long reads can now be generated for complete bacterial genome assembly. In this chapter, we describe a detailed MinION method to assemble a complete genome from a microorganism, polish the final assembly, and evaluate the genome quality using various software tools. Because of the low cost for MinION sequencing, this platform could be an asset for virtually any laboratory interested in generating complete genomes from microorganisms.

Indexed as

Genome, BacterialHigh-Throughput Nucleotide SequencingSoftwareBacteriaComputational BiologyDNA, BacterialGenomicsNanoporesNanopore SequencingSequence Analysis, DNAWhole Genome SequencingDNA, BacterialBacterial genomeLong-read assemblersOxford Nanopore

Identifiers

PMID39546195

What OpenQuestion holds

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Registered trials

None linked

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.