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Deciphering this information has the potential to greatly advance our understanding of genomic features and cellular functions. In comparison to other available sequencing methods, nanopore sequencing stands out due to its unique advantages of processing long nucleic acid strands in real time, within a small portable device, enabling the rapid analysis of samples in diverse settings. Evolving over the past decade, nanopore sequencing remains in a state of ongoing development and refinement, resulting in persistent challenges in protocols and technology. This article employs an interdisciplinary approach, evaluating experimental and computational methods to address critical gaps in our understanding in order to maximize the information gain from this advancing technology. Here, we present both overview and analysis of all aspects of nanopore sequencing by providing statistically supported insights. Thus, we aim to provide fresh perspectives on nanopore sequencing and give comprehensive guidelines for the diverse challenges that frequently impede optimal experimental outcomes.<\/jats:p>","DOI":"10.1093\/nar\/gkag023","type":"journal-article","created":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T12:38:36Z","timestamp":1769863116000},"source":"Crossref","is-referenced-by-count":8,"title":["Unlocking the full potential of nanopore sequencing: tips, tricks, and advanced data analysis techniques"],"prefix":"10.1093","volume":"54","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2006-4610","authenticated-orcid":false,"given":"Daria","family":"Meyer","sequence":"first","affiliation":[{"name":"RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University , Leutragraben 1 , 07743 Jena ,","place":["Germany"]},{"name":"Oncgnostics GmbH , L\u00f6bstedter Str. 41 , 07749 Jena ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Winfried","family":"Goettsch","sequence":"additional","affiliation":[{"name":"RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University , Leutragraben 1 , 07743 Jena ,","place":["Germany"]},{"name":"Leibniz Institute on Aging - 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