Locating patterns in Nanopore currents using time-warped signal representation of consensus nucleotides for demultiplexing and motif detection.

Abstract

Nanopore-based approaches for the sequencing of DNA and RNA molecules are promising technologies with potential applications in clinical genomics. These approaches have generated large numbers of time series objects over the years, however, it remains a challenge to accurately decipher the underlying nucleotide sequence corresponding to a given signal. By using a combination of consensus signal averaging and stream monitoring of variable-length motifs, we outline an online pattern matching framework that can efficiently locate consensus sequences in real world Nanopore datasets. We demonstrate the applicability of our proposed framework across two use-cases: demultiplexing of DNA barcodes and multiple motif site identification in RNA transcripts.