Genome Biology (Nov 2024)

TDFPS-Designer: an efficient toolkit for barcode design and selection in nanopore sequencing

  • Junhai Qi,
  • Zhengyi Li,
  • Yao-zhong Zhang,
  • Guojun Li,
  • Xin Gao,
  • Renmin Han

DOI
https://doi.org/10.1186/s13059-024-03423-3
Journal volume & issue
Vol. 25, no. 1
pp. 1 – 18

Abstract

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Abstract Oxford Nanopore Technologies (ONT) offers ultrahigh-throughput multi-sample sequencing but only provides barcode kits that enable up to 96-sample multiplexing. We present TDFPS-Designer, a new toolkit for nanopore sequencing barcode design, which creates significantly more barcodes: 137 with a length of 20 base pairs, 410 at 24 bp, and 1779 at 30 bp, far surpassing ONT’s offerings. It includes GPU-based acceleration for ultra-fast demultiplexing and designs robust barcodes suitable for high-error ONT data. TDFPS-Designer outperforms current methods, improving the demultiplexing recall rate by 20% relative to Guppy, without a reduction in precision.