HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing
Abstract 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...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2023-10-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13059-023-03053-1 |
| _version_ | 1797452487066648576 |
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| author | Renmin Han Junhai Qi Yang Xue Xiujuan Sun Fa Zhang Xin Gao Guojun Li |
| author_facet | Renmin Han Junhai Qi Yang Xue Xiujuan Sun Fa Zhang Xin Gao Guojun Li |
| author_sort | Renmin Han |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-03-09T15:09:23Z |
| format | Article |
| id | doaj.art-f95052921bfb475399ee29a4280824da |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-03-09T15:09:23Z |
| publishDate | 2023-10-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-f95052921bfb475399ee29a4280824da2023-11-26T13:29:15ZengBMCGenome Biology1474-760X2023-10-0124112910.1186/s13059-023-03053-1HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencingRenmin Han0Junhai Qi1Yang Xue2Xiujuan Sun3Fa Zhang4Xin Gao5Guojun Li6Research Center for Mathematics and Interdisciplinary Sciences, Shandong UniversityResearch Center for Mathematics and Interdisciplinary Sciences, Shandong UniversityResearch Center for Mathematics and Interdisciplinary Sciences, Shandong UniversityHigh Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of SciencesSchool of Medical Technolgoy, Beijing Institute of TechnologyKing Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) DivisionResearch Center for Mathematics and Interdisciplinary Sciences, Shandong UniversityAbstract 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.https://doi.org/10.1186/s13059-023-03053-1Nanopore sequencingDemultiplexingClustering |
| spellingShingle | Renmin Han Junhai Qi Yang Xue Xiujuan Sun Fa Zhang Xin Gao Guojun Li HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing Genome Biology Nanopore sequencing Demultiplexing Clustering |
| title | HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing |
| title_full | HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing |
| title_fullStr | HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing |
| title_full_unstemmed | HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing |
| title_short | HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing |
| title_sort | hycdemux a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing |
| topic | Nanopore sequencing Demultiplexing Clustering |
| url | https://doi.org/10.1186/s13059-023-03053-1 |
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