The year 2022 will be remembered as the turning point for accurate long-read sequencing, which now establishes the gold standard for speed and accuracy at competitive costs. We discuss the key bioinformatics techniques needed to power long reads across application areas and close with our vision for long-read sequencing over the coming years.
References
Nurk, S. et al. Science 376, 44–53 (2022).
Aganezov, S. et al. Science 376, eabl3533 (2022).
Gorzynski, J. E. et al. N. Engl. J. Med. 386, 700–702 (2022).
Hufford, M. B. et al. Science 373, 655–662 (2021).
Glinos, D. A. et al. Nature 608, 353–359 (2022).
Naish, M. et al. Science 374, eabi7489 (2021).
Gershman, A. et al. Science 376, eabj5089 (2022).
Goodwin, S., McPherson, J. D. & McCombie, W. R. Nat. Rev. Genet. 17, 333–351 (2016).
Wenger, A. M. et al. Nat. Biotechnol. 37, 1155–1162 (2019).
Silvestre-Ryan, J. & Holmes, I. Genome Biol. 22, 38 (2021).
Ekim, B., Berger, B. & Chikhi, R. Cell Syst. 12, 958–968.e6 (2021).
Baid, G. et al. Nat. Biotechnol. https://doi.org/10.1038/s41587-022-01435-7 (2022).
Furlan, M. et al. RNA Biol. 18 (Suppl. 1), 31–40 (2021).
Kovaka, S., Fan, Y., Ni, B., Timp, W. & Schatz, M. C. Nat. Biotechnol. 39, 431–441 (2021).
Payne, A. et al. Nat. Biotechnol. 39, 442–450 (2021).
Gamaarachchi, H. et al. Nat. Biotechnol. 40, 1026–1029 (2022).
Watson, M. & Warr, A. Nat. Biotechnol. 37, 124–126 (2019).
Rautiainen, M. et al. Preprint at bioRxiv https://doi.org/10.1101/2022.06.24.497523 (2022).
Ou, S. et al. Preprint at bioRxiv https://doi.org/10.1101/2022.10.09.511471 (2022).
Vollger, M. R., Kerpedjiev, P., Phillippy, A. M. & Eichler, E. E. Bioinformatics https://doi.org/10.1093/bioinformatics/btac018 (2022).
Sedlazeck, F. J. et al. Nat. Methods 15, 461–468 (2018).
Audano, P. A. et al. Cell 176, 663–675.e19 (2019).
Alonge, M. et al. Cell 182, 145–161.e23 (2020).
Sone, J. et al. Nat. Genet. 51, 1215–1221 (2019).
Della Coletta, R., Qiu, Y., Ou, S., Hufford, M. B. & Hirsch, C. N. Genome Biol. 22, 3 (2021).
Li, H. Bioinformatics 34, 3094–3100 (2018).
Marco-Sola, S., Moure, J. C., Moreto, M. & Espinosa, A. Bioinformatics 37, 456–463 (2021).
Kirsche, M. et al. Preprint at bioRxiv https://doi.org/10.1101/2021.05.27.445886 (2021).
Wyman, D. & Mortazavi, A. Bioinformatics 35, 340–342 (2019).
Kovaka, S. et al. Genome Biol. 20, 278 (2019).
Chen, Y. et al. Preprint at bioRxiv https://doi.org/10.1101/2021.04.21.440736 (2021).
Drexler, H. L. et al. Nat. Protoc. 16, 1343–1375 (2021).
Lebrigand, K., Magnone, V., Barbry, P. & Waldmann, R. Nat. Commun. 11, 4025 (2020).
Acknowledgements
We would like to thank all past and current members of the Schatz lab, as well as our long-read collaborators, especially Timour Baslan, Andrew Carroll, Jason Chin, Megan Dennis, Evan Eichler, Tom Gingeras, Mark Gerstein, Sara Goodwin, Ian Henderson, Candice Hirsch, Matthew Hufford, Alison Klein, Ben Langmead, Zach Lippman, Erich Jarvis, W. Richard McCombie, Rajiv McCoy, Karen Miga, Rachel O’Neill, Mihaela Pertea, Adam Phillippy, Fritz Sedlazeck, Steven Salzberg, Winston Timp, Eli Van Allen, Justin Zook, and many others. Finally, we would also like to thank the researchers at PacBio and Oxford Nanopore for their developments and collaborations. This work was supported in part by the US National Science Foundation (IOS-2216612, IOS-1758800), the US National Institutes of Health (U24HG010263, U41HG006620, U01CA253481), and the Human Frontier Science Program (RGP0025/2021).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing interests.
Rights and permissions
About this article
Cite this article
Kovaka, S., Ou, S., Jenike, K.M. et al. Approaching complete genomes, transcriptomes and epi-omes with accurate long-read sequencing. Nat Methods 20, 12–16 (2023). https://doi.org/10.1038/s41592-022-01716-8
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41592-022-01716-8
- Springer Nature America, Inc.
This article is cited by
-
ClusTrast: a short read de novo transcript isoform assembler guided by clustered contigs
BMC Bioinformatics (2024)
-
Genomes in clinical care
npj Genomic Medicine (2024)
-
A systematic comparison of human mitochondrial genome assembly tools
BMC Bioinformatics (2023)