Title | Unveiling microbial diversity: harnessing long-read sequencing technology. |
Publication Type | Journal Article |
Year of Publication | 2024 |
Authors | Agustinho, DP, Fu, Y, Menon, VK, Metcalf, GA, Treangen, TJ, Sedlazeck, FJ |
Journal | Nat Methods |
Date Published | 2024 Apr 30 |
ISSN | 1548-7105 |
Abstract | Long-read sequencing has recently transformed metagenomics, enhancing strain-level pathogen characterization, enabling accurate and complete metagenome-assembled genomes, and improving microbiome taxonomic classification and profiling. These advancements are not only due to improvements in sequencing accuracy, but also happening across rapidly changing analysis methods. In this Review, we explore long-read sequencing's profound impact on metagenomics, focusing on computational pipelines for genome assembly, taxonomic characterization and variant detection, to summarize recent advancements in the field and provide an overview of available analytical methods to fully leverage long reads. We provide insights into the advantages and disadvantages of long reads over short reads and their evolution from the early days of long-read sequencing to their recent impact on metagenomics and clinical diagnostics. We further point out remaining challenges for the field such as the integration of methylation signals in sub-strain analysis and the lack of benchmarks. |
DOI | 10.1038/s41592-024-02262-1 |
Alternate Journal | Nat Methods |
PubMed ID | 38689099 |
PubMed Central ID | 1483832 |
Grant List | 1U19AI144297 / / U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID) / 1U19AI144297 / / U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID) / 1U19AI144297 / / U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID) / 1U19AI144297 / / U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID) / P01-AI152999 / / U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID) / P01-AI152999 / / U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID) / III-2239114 / / National Science Foundation (NSF) / EF-2126387 / / National Science Foundation (NSF) / III-2239114 / / National Science Foundation (NSF) / |