HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing

doi:10.1186/s13059-023-03053-1

	HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing
	Han, Renmin 1; Qi, Junhai 1,2; Xue, Yang 1; Sun, Xiujuan 3; Zhang, Fa 4; Gao, Xin 5; Li, Guojun 1
	2023-10-05
发表期刊	GENOME BIOLOGY
ISSN	1474-760X
卷号	24 期号:1 页码:29
摘要	DNA barcodes enable Oxford Nanopore sequencing to sequence multiple barcoded DNA samples on a single flow cell. DNA sequences with the same barcode need to be grouped together through demultiplexing. As the number of samples increases, accurate demultiplexing becomes difficult. We introduce HycDemux, which incorporates a GPU-parallelized hybrid clustering algorithm that uses nanopore signals and DNA sequences for accurate data clustering, alongside a voting-based module to finalize the demultiplexing results. Comprehensive experiments demonstrate that our approach outperforms unsupervised tools in short sequence fragment clustering and performs more robustly than current state-of-the-art demultiplexing tools for complex multi-sample sequencing data.
关键词	Nanopore sequencing Demultiplexing Clustering
DOI	10.1186/s13059-023-03053-1
收录类别	SCI
语种	英语
资助项目	National Key Research and Development Program of China[2020YFA0712400] ; National Key Research and Development Program of China[2021YFF0704300] ; National Natural Science Foundation of China[62072280] ; National Natural Science Foundation of China[11931008] ; National Natural Science Foundation of China[61771009] ; National Natural Science Foundation of China[32241027] ; Natural Science Foundation of Shandong Province[ZR2023YQ057] ; King Abdullah University of Science and Technology (KAUST) Office of Research Administration (ORA)[FCC/1/1976-44-01] ; King Abdullah University of Science and Technology (KAUST) Office of Research Administration (ORA)[FCC/1/1976-45-01] ; King Abdullah University of Science and Technology (KAUST) Office of Research Administration (ORA)[REI/1/5234-01-01] ; King Abdullah University of Science and Technology (KAUST) Office of Research Administration (ORA)[REI/1/5414-01-01] ; King Abdullah University of Science and Technology (KAUST) Office of Research Administration (ORA)[URF/1/4352-01-01] ; open project of BGI-Shenzhen[BGIRSZ20220005]
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS类目	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS记录号	WOS:001082806400002
出版者	BMC
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/21102
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Zhang, Fa; Gao, Xin; Li, Guojun
作者单位	1.Shandong Univ, Res Ctr Math & Interdisciplinary Sci, Qingdao 266237, Peoples R China 2.BioMap Res, Menlo Pk, CA USA 3.Chinese Acad Sci, Inst Comp Technol, High Performance Comp Res Ctr, Beijing 100190, Peoples R China 4.Beijing Inst Technol, Sch Med Technol, Beijing 100085, Peoples R China 5.King Abdullah Univ Sci & Technol KAUST, Computat Biosci Res Ctr CBRC, Comp Elect & Math Sci & Engn CEMSE Div, Thuwal 23955, Saudi Arabia
推荐引用方式 GB/T 7714	Han, Renmin,Qi, Junhai,Xue, Yang,et al. HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing[J]. GENOME BIOLOGY,2023,24(1):29.
APA	Han, Renmin.,Qi, Junhai.,Xue, Yang.,Sun, Xiujuan.,Zhang, Fa.,...&Li, Guojun.(2023).HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing.GENOME BIOLOGY,24(1),29.
MLA	Han, Renmin,et al."HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing".GENOME BIOLOGY 24.1(2023):29.