Nanopore sequencers can be used to selectively sequence certain DNA molecules in a pool by reversing the voltage across individual nanopores to reject specific sequences, enabling enrichment and depletion to address biological questions. Previously, we achieved this using dynamic time warping to map the signal to a reference genome, but the method required substantial computational resources and did not scale to gigabase-sized references. Here we overcome this limitation by using graphical processing unit (GPU) base-calling. We show enrichment of specific chromosomes from the human genome and of low-abundance organisms in mixed populations without a priori knowledge of sample composition. Finally, we enrich targeted panels comprising 25,600 exons from 10,000 human genes and 717 genes implicated in cancer, identifying PML–RARA fusions in the NB4 cell line in <15 h sequencing. These methods can be used to efficiently screen any target panel of genes without specialized sample preparation using any computer and a suitable GPU. Our toolkit, readfish, is available at https://www.github.com/looselab/readfish.

纳米孔测序仪可用于选择性地对池中的某些 DNA 分子进行测序，方法是反转各个纳米孔上的电压以拒绝特定序列，从而实现富集和耗尽以解决生物学问题。此前，我们使用动态时间扭曲将信号映射到参考基因组来实现这一目标，但该方法需要大量的计算资源，并且无法扩展到千兆碱基大小的参考。在这里，我们通过使用图形处理单元 (GPU) 碱基识别克服了这一限制。我们展示了人类基因组中特定染色体的富集以及混合群体中低丰度生物体的富集，而无需先验了解样本组成。最后，我们丰富了包含来自 10,000 个人类基因的 25,600 个外显子和与癌症相关的 717 个基因的靶向面板，在 15 小时内测序鉴定了 NB4 细胞系中的PML – RARA融合。这些方法可用于有效筛选任何目标基因组，无需使用任何计算机和合适的 GPU 进行专门的样品制备。我们的工具包 readfish 可从 https://www.github.com/looselab/readfish 获取。