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

文献类型：期刊论文

作者Han, Renmin5; Qi, Junhai3,5; Xue, Yang5; Sun, Xiujuan4; Zhang, Fa1; Gao, Xin2; Li, Guojun5
刊名GENOME BIOLOGY
出版日期2023-10-05
卷号24期号:1页码:29
ISSN号1474-760X
关键词Nanopore sequencing Demultiplexing Clustering
DOI10.1186/s13059-023-03053-1
英文摘要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.
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
语种英语
出版者BMC
WOS记录号WOS:001082806400002
源URL[http://119.78.100.204/handle/2XEOYT63/21101]  
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.Beijing Inst Technol, Sch Med Technol, Beijing 100085, Peoples R China
2.King Abdullah Univ Sci & Technol KAUST, Computat Biosci Res Ctr CBRC, Comp Elect & Math Sci & Engn CEMSE Div, Thuwal 23955, Saudi Arabia
3.BioMap Res, Menlo Pk, CA USA
4.Chinese Acad Sci, Inst Comp Technol, High Performance Comp Res Ctr, Beijing 100190, Peoples R China
5.Shandong Univ, Res Ctr Math & Interdisciplinary Sci, Qingdao 266237, Peoples R China
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.

入库方式： OAI收割

来源：计算技术研究所

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