PBSIM3: a simulator for all types of PacBio and ONT long reads-Reference-Cited by-同舟云学术

PBSIM3: a simulator for all types of PacBio and ONT long reads

Published:2022-10-06 Issue:4 Volume:4 Page:
ISSN:2631-9268
Container-title:NAR Genomics and Bioinformatics
language:en
Short-container-title:

Author:

Ono Yukiteru¹^ORCID,Hamada Michiaki²³⁴⁵^ORCID,Asai Kiyoshi¹⁶^ORCID

Affiliation:

1. Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo , 5-1-5 Kashiwanoha, Kashiwa 277-8561, Japan

2. Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University , 55N-06-10, 3-4-1, Okubo, Shinjuku-ku, Tokyo 169-8555, Japan

3. Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST) , 63-520, 3-4-1, Okubo, Shinjuku-ku, Tokyo 169-8555, Japan

4. Institute for Medical-Oriented Structural Biology, Waseda University , 2-2, Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan

5. Graduate School of Medicine, Nippon Medical School , 1-1-5, Sendagi, Bunkyo-ku, Tokyo, 113-8602, Japan

6. Artificial Intelligence Research Center (AIRC), National Institute of Advanced Industrial Science and Technology (AIST) , 2-3-26, Aomi, Koto-ku, 135-0064 Tokyo, Japan

Abstract

AbstractLong-read sequencers, such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) sequencers, have improved their read length and accuracy, thereby opening up unprecedented research. Many tools and algorithms have been developed to analyze long reads, and rapid progress in PacBio and ONT has further accelerated their development. Together with the development of high-throughput sequencing technologies and their analysis tools, many read simulators have been developed and effectively utilized. PBSIM is one of the popular long-read simulators. In this study, we developed PBSIM3 with three new functions: error models for long reads, multi-pass sequencing for high-fidelity read simulation and transcriptome sequencing simulation. Therefore, PBSIM3 is now able to meet a wide range of long-read simulation requirements.

Funder

JSPS

Publisher

Oxford University Press (OUP)

Subject

Applied Mathematics,Computer Science Applications,Genetics,Molecular Biology,Structural Biology

Link

https://academic.oup.com/nargab/article-pdf/4/4/lqac092/49289543/lqac092.pdf

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