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Accurate k-mer Classification Using Read Profiles

Authors Yoshihiko Suzuki , Gene Myers

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Author Details

Yoshihiko Suzuki
  • Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
Gene Myers
  • Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
  • Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
  • Center for Systems Biology Dresden, Dresden, Germany

Acknowledgements

We wish to thank Shinichi Morishita, Yuta Suzuki, Bansho Masutani, Ryo Nakabayashi, Charles Plessy, and Michael Mansfield for their feedback and stimulating works. We also thank the Scientific Computing and Data Analysis section of Research Support Division and Communication and Public Relations Division at OIST for providing HPC resources and for proofreading of the manuscript, respectively.

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Yoshihiko Suzuki and Gene Myers. Accurate k-mer Classification Using Read Profiles. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 10:1-10:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
https://doi.org/10.4230/LIPIcs.WABI.2022.10

Abstract

Contiguous strings of length k, called k-mers, are a fundamental element in many bioinformatics tasks. The number of occurrences of a k-mer in a given set of DNA sequencing reads, its k-mer count, has often been used to roughly estimate the copy number of a k-mer in the genome from which the reads were sampled. The problem of estimating copy numbers, called here the k-mer classification problem, has been based on simply analyzing the histogram of counts of all the k-mers in a data set, thus ignoring the positional context and dependency between multiple k-mers that appear nearby in the underlying genome. Here we present an efficient and significantly more accurate method for classifying k-mers by analyzing the sequence of k-mer counts along each sequencing read, called a read profile. By analyzing read profiles, we explicitly incorporate into the model the dependencies between the positionally adjacent k-mers and the sequence context-dependent error rates estimated from the given dataset. For long sequencing reads produced with the accurate high-fidelity (HiFi) sequencing technology, an implementation of our method, ClassPro, outperforms the conventional, histogram-based method in every simulation dataset of fruit fly and human with various realistic values of sequencing coverage and heterozygosity. Within only a few minutes, ClassPro achieves an average accuracy of > 99.99% across reads without repetitive k-mers and > 99.5% across all reads, in a typical fruit fly simulation data set with a 40× coverage. The resulting, more accurate k-mer classifications by ClassPro are in principle expected to improve any k-mer-based downstream analyses for sequenced reads such as read mapping and overlap, spectral alignment and error correction, haplotype phasing, and trio binning to name but a few. ClassPro is available at https://github.com/yoshihikosuzuki/ClassPro.

Subject Classification

ACM Subject Classification
  • Applied computing → Molecular sequence analysis
Keywords
  • K-mer
  • K-mer count
  • K-mer classification
  • HiFi sequencing

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