Evaluation of simulation models to mimic the distortions introduced into squiggles by nanopore sequencers and segmentation algorithms.

ABSTRACT: Nucleotides ratcheted through the biomolecular pores of nanopore sequencers generate raw picoamperage currents, which are segmented into step-current level signals representing the nucleotide sequence. These 'squiggles' are a noisy, distorted representation of the underlying true stepped current levels due to experimental and algorithmic factors. We were interested in developing a simulation model to support a white-box approach to identify common distortions, rather than relying on commonly used black box neural network techniques for basecalling nanopore signals. Dynamic time warped-space averaging (DTWA) techniques can generate a consensus from multiple noisy signals without introducing key feature distortions that occur with standard averaging. As a preprocessing tool, DTWA could provi

SUBMITTER: Smith M 

PROVIDER: S-EPMC6638935 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature