Satam H, Joshi K, Mangrolia U, Waghoo S, Zaidi G, Rawool S, et al. Next-generation sequencing technology: current trends and advancements. Biology (Basel). 2023;12(7):997.

CAS  PubMed  Google Scholar 

van Dijk EL, Naquin D, Gorrichon K, Jaszczyszyn Y, Ouazahrou R, Thermes C, et al. Genomics in the long-read sequencing era. Trends Genet. 2023;39(9):649–71.

Article  PubMed  Google Scholar 

Warburton PE, Sebra RP. Long-read DNA sequencing: recent advances and remaining challenges. Annu Rev Genomics Hum Genet. 2023;24:109–32.

Article  CAS  PubMed  Google Scholar 

Ciuffreda L, Rodríguez-Pérez H, Flores C. Nanopore sequencing and its application to the study of microbial communities. Comput Struct Biotechnol J. 2021;19:1497–511.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Oehler JB, Wright H, Stark Z, Mallett AJ, Schmitz U. The application of long-read sequencing in clinical settings. Hum Genomics. 2023;17(1):73.

Article  PubMed  PubMed Central  Google Scholar 

Wasswa FB, Kassaza K, Nielsen K, Bazira J. MinION whole-genome sequencing in resource-limited settings: challenges and opportunities. Curr Clin Microb Rep. 2022;9(4):52–9.

Article  Google Scholar 

Olivucci G, Iovino E, Innella G, Turchetti D, Pippucci T, Magini P. Long read sequencing on its way to the routine diagnostics of genetic diseases. Front Genet. 2024;15:1374860.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Liu Z, Xie Z, Li M. Comprehensive and deep evaluation of structural variation detection pipelines with third-generation sequencing data. Genome Biol. 2024;25(1):188.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cohen KA, Manson AL, Desjardins CA, Abeel T, Earl AM. Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges. Genome Medicine. 2019;11(1):45.

Article  PubMed  PubMed Central  Google Scholar 

Gross MR, Hsu R, Deitsch KW. Evolution of transcriptional control of antigenic variation and virulence in human and ape malaria parasites. BMC Ecol Evol. 2021;21(1):139.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhang X, Deitsch KW, Kirkman LA. The contribution of extrachromosomal DNA to genome plasticity in malaria parasites. Mol Microbiol. 2021;115(4):503–7.

Article  CAS  PubMed  Google Scholar 

Chera A, Stancu-Cretu M, Zabet NR, Bucur O. Shedding light on DNA methylation and its clinical implications: the impact of long-read-based nanopore technology. Epigenetics Chromatin. 2024;17(1):39.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dilthey AT, Jain C, Koren S, Phillippy AM. Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps. Nat Commun. 2019;10(1):3066.

Article  PubMed  PubMed Central  Google Scholar 

Amarasinghe SL, Su S, Dong X, Zappia L, Ritchie ME, Gouil Q. Opportunities and challenges in long-read sequencing data analysis. Genome Biol. 2020;21(1):30.

Article  PubMed  PubMed Central  Google Scholar 

Espinosa E, Bautista R, Larrosa R, Plata O. Advancements in long-read genome sequencing technologies and algorithms. Genomics. 2024;116(3):110842.

Article  CAS  PubMed  Google Scholar 

Hon T, Mars K, Young G, Tsai Y-C, Karalius JW, Landolin JM, et al. Highly accurate long-read HiFi sequencing data for five complex genomes. Sci Data. 2020;7(1):399.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pagès-Gallego M, de Ridder J. Comprehensive benchmark and architectural analysis of deep learning models for nanopore sequencing basecalling. Genome Biol. 2023;24(1):71.

Article  PubMed  PubMed Central  Google Scholar 

Wang Y, Zhao Y, Bollas A, Wang Y, Au KF. Nanopore sequencing technology, bioinformatics and applications. Nat Biotechnol. 2021;39(11):1348–65.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Xu Z, Mai Y, Liu D, He W, Lin X, Xu C, et al. Fast-bonito: a faster deep learning based basecaller for nanopore sequencing. Artif Intell Life Sci. 2021;1:100011.

CAS  Google Scholar 

Martin S, Heavens D, Lan Y, Horsfield S, Clark MD, Leggett RM. Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples. Genome Biol. 2022;23(1):11.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Baid G, Cook DE, Shafin K, Yun T, Llinares-López F, Berthet Q, et al. DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer. Nat Biotechnol. 2023;41(2):232–8.

CAS  PubMed  Google Scholar 

Chen Y, Mao L, Lai D, Xu W, Zhang Y, Wu S, et al. Improved targeting of the 16S rDNA nanopore sequencing method enables rapid pathogen identification in bacterial pneumonia in children. Front Cell Infect Microbiol. 2023;12:1001607.

Article  PubMed  PubMed Central  Google Scholar 

Han H-S, Ro DH, Chung J, Kim N, Moon J. Nanopore 16S amplicon sequencing enables rapid detection of pathogen in knee periprosthetic joint infection. Int J Med Microbiol. 2022;312(8):151570.

Article  CAS  PubMed  Google Scholar 

Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017;13(6):e1005595.

Article  PubMed  PubMed Central  Google Scholar 

Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019;37(5):540–6.

Article  CAS  PubMed  Google Scholar 

Park SY, Faraci G, Ward P, Lee HY. Utilizing cost-effective portable equipment to enhance COVID-19 variant tracking both on-site and at a large scale. J Clin Microbiol. 2024;62(4):e0155823.

Article  PubMed  Google Scholar 

Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics. 2018;34(23):4121–3.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li P-E, Lo C-C, Anderson JJ, Davenport KW, Bishop-Lilly KA, Xu Y, et al. Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform. Nucleic Acids Res. 2016;45(1):67–80.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Koppad S, B A, Gkoutos GV, Acharjee A. Cloud computing enabled big multi-omics data analytics. Bioinform Biol Insights. 2021;15:11779322211035920.

Article  PubMed  PubMed Central  Google Scholar 

Hoang MTV, Irinyi L, Hu Y, Schwessinger B, Meyer W. Long-reads-based metagenomics in clinical diagnosis with a special focus on fungal infections. Front Microbiol. 2021;12:708550.

Article  PubMed  Google Scholar 

Wu CT, Shropshire WC, Bhatti MM, Cantu S, Glover IK, Anand SS, et al. Rapid whole genome characterization of high-risk pathogens using long-read sequencing to identify potential healthcare transmission. medRxiv. 2024. https://doi.org/10.1101/2024.08.19.24312266.

Zhao W, Zeng W, Pang B, Luo M, Peng Y, Xu J, et al. Oxford nanopore long-read sequencing enables the generation of complete bacterial and plasmid genomes without short-read sequencing. Front Microbiol. 2023;14:1179966.

Article