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Calling Homopolymer Stretches from Raw Nanopore Reads by Analyzing k-mer Dwell Times

  • Peter SarkozyEmail author
  • Ákos Jobbágy
  • Peter Antal
Conference paper
Part of the IFMBE Proceedings book series (IFMBE, volume 65)

Abstract

Oxford Nanopore Technologies’ (ONT) MinION device is capable of reading single molecule DNA strands tens of thousands of bases long, by passing a strand through a nanopore and recording the changes in electric current. The error rate of the platform is higher than most mature next-generation sequencing (NGS) platforms, with many of the deletions accumulating in stretches of identical bases (homopolymers). However, the mean time each 5-base long subsequence (k-mer) of the molecule spends inside of the pore (dwell time) can also be used to infer the length of the true sequence. We developed a method called NanoTimer, which estimates the homopolymer length from the dwell times. It relies on the redundancy of having multiple reads covering a reference sequence, and the depth of coverage determines its accuracy.

Keywords

Nanopore Sequencing Homopolymer Indel Dwell time 

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Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  1. 1.Department of Information and Measurement SystemsBudapest University of TechnologyBudapestHungary

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