Open Access
Open access
International Journal of Molecular Sciences, том 23, издание 15, номер публикации: 8569

Nanopore Sequencing for De Novo Bacterial Genome Assembly and Search for Single-Nucleotide Polymorphism

Тип документаJournal Article
Дата публикации2022-08-02
ИздательMultidisciplinary Digital Publishing Institute (MDPI)
Название журналаInternational Journal of Molecular Sciences
Квартиль по SCImagoQ1
Квартиль по Web of ScienceQ1
Импакт-фактор 20216.21
ISSN16616596, 14220067
Organic Chemistry
Inorganic Chemistry
Physical and Theoretical Chemistry
Computer Science Applications
Molecular Biology
General Medicine
Краткое описание
Nanopore sequencing (ONT) is a new and rapidly developing method for determining nucleotide sequences in DNA and RNA. It serves the ability to obtain long reads of thousands of nucleotides without assembly and amplification during sequencing compared to next-generation sequencing. Nanopore sequencing can help for determination of genetic changes leading to antibiotics resistance. This study presents the application of ONT technology in the assembly of an E. coli genome characterized by a deletion of the tolC gene and known single-nucleotide variations leading to antibiotic resistance, in the absence of a reference genome. We performed benchmark studies to determine minimum coverage depth to obtain a complete genome, depending on the quality of the ONT data. A comparison of existing programs was carried out. It was shown that the Flye program demonstrates plausible assembly results relative to others (Shasta, Canu, and Necat). The required coverage depth for successful assembly strongly depends on the size of reads. When using high-quality samples with an average read length of 8 Kbp or more, the coverage depth of 30× is sufficient to assemble the complete genome de novo and reliably determine single-nucleotide variations in it. For samples with shorter reads with mean lengths of 2 Kbp, a higher coverage depth of 50× is required. Avoiding of mechanical mixing is obligatory for samples preparation. Nanopore sequencing can be used alone to determine antibiotics-resistant genetic features of bacterial strains.
Пристатейные ссылки: 38
Insights into applications and strategies for discovery of microbial bioactive metabolites.
Maithani D., Sharma A., Gangola S., Chaudhary P., Bhatt P.
Q2 Microbiological Research 2022 цитирований: 0
Initial Analysis of Structural Variation Detections in Cattle Using Long-Read Sequencing Methods
Gao Y., Ma L., Liu G.E.
Q2 Genes 2022 цитирований: 0
Open Access
Open access
Complete Genome Sequences of Four Isolated Bacteria from an Undergraduate Microbiology Course Using a Hybrid Assembly Approach
Sanders C.I., Ne Ville C.J., Orwin P.M.
Q3 Microbiology Resource Announcements 2022 цитирований: 0
New strategies to improve minimap2 alignment accuracy
Li H.
Q1 Bioinformatics 2021 цитирований: 35
Exploring Semi-Quantitative Metagenomic Studies Using Oxford Nanopore Sequencing: A Computational and Experimental Protocol
Alili R., Belda E., Le P., Wirth T., Zucker J., Prifti E., Clément K.
Q2 Genes 2021 цитирований: 2
Open Access
Open access
Comparison of De Novo Assembly Strategies for Bacterial Genomes
Zhang P., Jiang D., Wang Y., Yao X., Luo Y., Yang Z.
Q1 International Journal of Molecular Sciences 2021 цитирований: 7
Open Access
Open access
MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction
Murigneux V., Roberts L.W., Forde B.M., Phan M., Nhu N.T., Irwin A.D., Harris P.N., Paterson D.L., Schembri M.A., Whiley D.M., Beatson S.A.
Q1 BMC Genomics 2021 цитирований: 5
Open Access
Open access
Rapid nanopore-based DNA sequencing protocol of antibiotic-resistant bacteria for use in surveillance and outbreak investigation
Ferreira F.A., Helmersen K., Visnovska T., Jørgensen S.B., Aamot H.V.
Q1 Microbial genomics 2021 цитирований: 8
Open Access
Open access
Long-Read Sequencing Improves the Detection of Structural Variations Impacting Complex Non-Coding Elements of the Genome
Begum G., Albanna A., Bankapur A., Nassir N., Tambi R., Berdiev B.K., Akter H., Karuvantevida N., Kellam B., Alhashmi D., Sung W.W., Thiruvahindrapuram B., Alsheikh-Ali A., Scherer S.W., Uddin M.
Q1 International Journal of Molecular Sciences 2021 цитирований: 7
Open Access
Open access
Twelve years of SAMtools and BCFtools
Danecek P., Bonfield J.K., Liddle J., Marshall J., Ohan V., Pollard M.O., Whitwham A., Keane T., McCarthy S.A., Davies R.M., Li H.
Q1 GigaScience 2021 цитирований: 1171
Open Access
Open access
Efficient assembly of nanopore reads via highly accurate and intact error correction
Chen Y., Nie F., Xie S., Zheng Y., Dai Q., Bray T., Wang Y., Xing J., Huang Z., Wang D., He L., Luo F., Wang J., Liu Y., Xiao C.
Q1 Nature Communications 2021 цитирований: 63
Open Access
Open access
A Long-Read Sequencing Approach for Direct Haplotype Phasing in Clinical Settings
Maestri S., Maturo M.G., Cosentino E., Marcolungo L., Iadarola B., Fortunati E., Rossato M., Delledonne M.
Q1 International Journal of Molecular Sciences 2020 цитирований: 8
Open Access
Open access
Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes
Fatima N., Petri A., Gyllensten U., Feuk L., Ameur A.
Q2 Genes 2020 цитирований: 3
Open Access
Open access
metaFlye: scalable long-read metagenome assembly using repeat graphs.
Kolmogorov M., Bickhart D.M., Behsaz B., Gurevich A., Rayko M., Shin S.B., Kuhn K., Yuan J., Polevikov E., Smith T.P., Pevzner P.A.
Q1 Nature Methods 2020 цитирований: 186
Benchmarking hybrid assembly approaches for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing
Chen Z., Erickson D.L., Meng J.
Q1 BMC Genomics 2020 цитирований: 15
Open Access
Open access


1. Khrenova M. G. и др. Nanopore Sequencing for De Novo Bacterial Genome Assembly and Search for Single-Nucleotide Polymorphism // International Journal of Molecular Sciences. 2022. Т. 23. № 15. С. 8569.


DO - 10.3390/ijms23158569

UR -

TI - Nanopore Sequencing for De Novo Bacterial Genome Assembly and Search for Single-Nucleotide Polymorphism

T2 - International Journal of Molecular Sciences

AU - Khrenova, Maria G.

AU - Panova, Tatiana V.

AU - Rodin, Vladimir A.

AU - Kryakvin, Maxim A.

AU - Lukyanov, Dmitrii A.

AU - Osterman, Ilya A.

AU - Zvereva, Maria I.

PY - 2022

DA - 2022/08/02


SP - 8569

IS - 15

VL - 23

SN - 1422-0067

ER -

BibTex |


doi = {10.3390/ijms23158569},

url = {},

year = 2022,

month = {aug},

publisher = {{MDPI} {AG}},

volume = {23},

number = {15},

pages = {8569},

author = {Maria G. Khrenova and Tatiana V. Panova and Vladimir A. Rodin and Maxim A. Kryakvin and Dmitrii A. Lukyanov and Ilya A. Osterman and Maria I. Zvereva},

title = {Nanopore Sequencing for De Novo Bacterial Genome Assembly and Search for Single-Nucleotide Polymorphism},

journal = {International Journal of Molecular Sciences}


Khrenova, Maria G., et al. “Nanopore Sequencing for De Novo Bacterial Genome Assembly and Search for Single-Nucleotide Polymorphism.” International Journal of Molecular Sciences, vol. 23, no. 15, Aug. 2022, p. 8569. Crossref,