Comparison of the Nanopore and PacBio sequencing technologies for DNA 5-methylcytosine detection

Yadong Liu; Zhongyu Liu; Tao Jiang; Tianyi Zang; Yadong Wang

doi:10.1109/BIBM55620.2022.9995567

Comparison of the Nanopore and PacBio sequencing technologies for DNA 5-methylcytosine detection

Yadong Liu
, Zhongyu Liu
, Tao Jiang^*
, Tianyi Zang^*
, Yadong Wang^*

^*Corresponding author for this work

Faculty of Computing, Harbin Institute of Technology

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

5 Scopus citations

Abstract

DNA methylation provides a pivotal layer of epigenetic regulation in eukaryotes that has significant involvement for numerous biological processes in health and disease. Recent long-read sequencing technology including Oxford Nanopore sequencing and PacBio HiFi sequencing greatly expands the capacity of long-range, single-molecule, and direct DNA modification detection from reads without extra laboratory techniques. A growing number of analytical pipelines including base-calling and 5mC methylation detection have been developed, but there is still a lack of comprehensive evaluations of the two sequencing technologies. Here, we assess the performance of different methylation-calling pipelines based on Nanopore and HiFi sequencing datasets to provide a systematic evaluation to guide researchers on how to select the long-read sequencing technologies in performing human epigenome-wide studies.

Original language	English
Title of host publication	Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022
Editors	Donald Adjeroh, Qi Long, Xinghua Shi, Fei Guo, Xiaohua Hu, Srinivas Aluru, Giri Narasimhan, Jianxin Wang, Mingon Kang, Ananda M. Mondal, Jin Liu
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	220-225
Number of pages	6
ISBN (Electronic)	9781665468190
DOIs	https://doi.org/10.1109/BIBM55620.2022.9995567
State	Published - 2022
Externally published	Yes
Event	2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022 - Las Vegas, United States Duration: 6 Dec 2022 → 8 Dec 2022

Publication series

Name	Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022

Conference

Conference	2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022
Country/Territory	United States
City	Las Vegas
Period	6/12/22 → 8/12/22

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

evaluation
long-read sequencing
methylation

Access to Document

10.1109/BIBM55620.2022.9995567

Cite this

Liu, Y., Liu, Z., Jiang, T., Zang, T., & Wang, Y. (2022). Comparison of the Nanopore and PacBio sequencing technologies for DNA 5-methylcytosine detection. In D. Adjeroh, Q. Long, X. Shi, F. Guo, X. Hu, S. Aluru, G. Narasimhan, J. Wang, M. Kang, A. M. Mondal, & J. Liu (Eds.), Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022 (pp. 220-225). (Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM55620.2022.9995567

Liu, Yadong ; Liu, Zhongyu ; Jiang, Tao et al. / Comparison of the Nanopore and PacBio sequencing technologies for DNA 5-methylcytosine detection. Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022. editor / Donald Adjeroh ; Qi Long ; Xinghua Shi ; Fei Guo ; Xiaohua Hu ; Srinivas Aluru ; Giri Narasimhan ; Jianxin Wang ; Mingon Kang ; Ananda M. Mondal ; Jin Liu. Institute of Electrical and Electronics Engineers Inc., 2022. pp. 220-225 (Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022).

@inproceedings{0008d0c94b5149f097cd782a5b02b8b1,

title = "Comparison of the Nanopore and PacBio sequencing technologies for DNA 5-methylcytosine detection",

abstract = "DNA methylation provides a pivotal layer of epigenetic regulation in eukaryotes that has significant involvement for numerous biological processes in health and disease. Recent long-read sequencing technology including Oxford Nanopore sequencing and PacBio HiFi sequencing greatly expands the capacity of long-range, single-molecule, and direct DNA modification detection from reads without extra laboratory techniques. A growing number of analytical pipelines including base-calling and 5mC methylation detection have been developed, but there is still a lack of comprehensive evaluations of the two sequencing technologies. Here, we assess the performance of different methylation-calling pipelines based on Nanopore and HiFi sequencing datasets to provide a systematic evaluation to guide researchers on how to select the long-read sequencing technologies in performing human epigenome-wide studies.",

keywords = "evaluation, long-read sequencing, methylation",

author = "Yadong Liu and Zhongyu Liu and Tao Jiang and Tianyi Zang and Yadong Wang",

note = "Publisher Copyright: {\textcopyright} 2022 IEEE.; 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022 ; Conference date: 06-12-2022 Through 08-12-2022",

year = "2022",

doi = "10.1109/BIBM55620.2022.9995567",

language = "英语",

series = "Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022",

publisher = "Institute of Electrical and Electronics Engineers Inc.",

pages = "220--225",

editor = "Donald Adjeroh and Qi Long and Xinghua Shi and Fei Guo and Xiaohua Hu and Srinivas Aluru and Giri Narasimhan and Jianxin Wang and Mingon Kang and Mondal, \{Ananda M.\} and Jin Liu",

booktitle = "Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022",

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}

Liu, Y, Liu, Z, Jiang, T , Zang, T & Wang, Y 2022, Comparison of the Nanopore and PacBio sequencing technologies for DNA 5-methylcytosine detection. in D Adjeroh, Q Long, X Shi, F Guo, X Hu, S Aluru, G Narasimhan, J Wang, M Kang, AM Mondal & J Liu (eds), Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022. Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022, Institute of Electrical and Electronics Engineers Inc., pp. 220-225, 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022, Las Vegas, United States, 6/12/22. https://doi.org/10.1109/BIBM55620.2022.9995567

Comparison of the Nanopore and PacBio sequencing technologies for DNA 5-methylcytosine detection. / Liu, Yadong; Liu, Zhongyu; Jiang, Tao et al.
Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022. ed. / Donald Adjeroh; Qi Long; Xinghua Shi; Fei Guo; Xiaohua Hu; Srinivas Aluru; Giri Narasimhan; Jianxin Wang; Mingon Kang; Ananda M. Mondal; Jin Liu. Institute of Electrical and Electronics Engineers Inc., 2022. p. 220-225 (Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - Comparison of the Nanopore and PacBio sequencing technologies for DNA 5-methylcytosine detection

AU - Liu, Yadong

AU - Liu, Zhongyu

AU - Jiang, Tao

AU - Zang, Tianyi

AU - Wang, Yadong

PY - 2022

Y1 - 2022

N2 - DNA methylation provides a pivotal layer of epigenetic regulation in eukaryotes that has significant involvement for numerous biological processes in health and disease. Recent long-read sequencing technology including Oxford Nanopore sequencing and PacBio HiFi sequencing greatly expands the capacity of long-range, single-molecule, and direct DNA modification detection from reads without extra laboratory techniques. A growing number of analytical pipelines including base-calling and 5mC methylation detection have been developed, but there is still a lack of comprehensive evaluations of the two sequencing technologies. Here, we assess the performance of different methylation-calling pipelines based on Nanopore and HiFi sequencing datasets to provide a systematic evaluation to guide researchers on how to select the long-read sequencing technologies in performing human epigenome-wide studies.

AB - DNA methylation provides a pivotal layer of epigenetic regulation in eukaryotes that has significant involvement for numerous biological processes in health and disease. Recent long-read sequencing technology including Oxford Nanopore sequencing and PacBio HiFi sequencing greatly expands the capacity of long-range, single-molecule, and direct DNA modification detection from reads without extra laboratory techniques. A growing number of analytical pipelines including base-calling and 5mC methylation detection have been developed, but there is still a lack of comprehensive evaluations of the two sequencing technologies. Here, we assess the performance of different methylation-calling pipelines based on Nanopore and HiFi sequencing datasets to provide a systematic evaluation to guide researchers on how to select the long-read sequencing technologies in performing human epigenome-wide studies.

KW - evaluation

KW - long-read sequencing

KW - methylation

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DO - 10.1109/BIBM55620.2022.9995567

M3 - 会议稿件

AN - SCOPUS:85146717628

T3 - Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022

SP - 220

EP - 225

BT - Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022

A2 - Adjeroh, Donald

A2 - Long, Qi

A2 - Shi, Xinghua

A2 - Guo, Fei

A2 - Hu, Xiaohua

A2 - Aluru, Srinivas

A2 - Narasimhan, Giri

A2 - Wang, Jianxin

A2 - Kang, Mingon

A2 - Mondal, Ananda M.

A2 - Liu, Jin

PB - Institute of Electrical and Electronics Engineers Inc.

T2 - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022

Y2 - 6 December 2022 through 8 December 2022

ER -

Liu Y, Liu Z, Jiang T , Zang T , Wang Y. Comparison of the Nanopore and PacBio sequencing technologies for DNA 5-methylcytosine detection. In Adjeroh D, Long Q, Shi X, Guo F, Hu X, Aluru S, Narasimhan G, Wang J, Kang M, Mondal AM, Liu J, editors, Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022. Institute of Electrical and Electronics Engineers Inc. 2022. p. 220-225. (Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022). doi: 10.1109/BIBM55620.2022.9995567

Comparison of the Nanopore and PacBio sequencing technologies for DNA 5-methylcytosine detection

Abstract

Publication series

Conference

UN SDGs

Keywords

Access to Document

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