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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 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.

SUBMITTER: Han R

PROVIDER: S-EPMC10552309 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature

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

Han Renmin R Qi Junhai J Xue Yang Y Sun Xiujuan X Zhang Fa F Gao Xin X Li Guojun G

Genome biology 20231005 1

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 demultipl ...[more]

PMID: 37798751

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