Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED

Abstract

ReadUntil sequencing allows nanopore devices to selectively eject individual reads from the pore in real-time. This could enable purely computational targeted sequencing, however most mapping methods require basecalling, which is computationally intensive. Here we present UNCALLED (github.com/skovaka/UNCALLED), an open-source mapper that rapidly matches streaming nanopore current signals to a reference sequence. UNCALLED probabilistically considers k-mers that the signal could represent, and then prunes the candidates based on the reference encoded within an FM-index. We used UNCALLED to deplete sequencing of known bacterial genomes within a metagenomics community, enriching the remaining species by 4.46 fold. UNCALLED also enriched 148 human genes associated with hereditary cancers to 29.6x coverage using one MinION flowcell, enabling accurate detection of SNPs, indels, structural variants (SVs), and methylation in these genes. Twice as many SVs were detected compared to 50x coverage Illumina sequencing, all verified by whole-genome nanopore and PacBio HiFi sequencing.