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Minimum error correction-based haplotype assembly: Considerations for long read data

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  • Sina Majidian
  • Mohammad Hossein Kahaei
  • Dick de Ridder

Abstract

The single nucleotide polymorphism (SNP) is the most widely studied type of genetic variation. A haplotype is defined as the sequence of alleles at SNP sites on each haploid chromosome. Haplotype information is essential in unravelling the genome-phenotype association. Haplotype assembly is a well-known approach for reconstructing haplotypes, exploiting reads generated by DNA sequencing devices. The Minimum Error Correction (MEC) metric is often used for reconstruction of haplotypes from reads. However, problems with the MEC metric have been reported. Here, we investigate the MEC approach to demonstrate that it may result in incorrectly reconstructed haplotypes for devices that produce error-prone long reads. Specifically, we evaluate this approach for devices developed by Illumina, Pacific BioSciences and Oxford Nanopore Technologies. We show that imprecise haplotypes may be reconstructed with a lower MEC than that of the exact haplotype. The performance of MEC is explored for different coverage levels and error rates of data. Our simulation results reveal that in order to avoid incorrect MEC-based haplotypes, a coverage of 25 is needed for reads generated by Pacific BioSciences RS systems.

Suggested Citation

  • Sina Majidian & Mohammad Hossein Kahaei & Dick de Ridder, 2020. "Minimum error correction-based haplotype assembly: Considerations for long read data," PLOS ONE, Public Library of Science, vol. 15(6), pages 1-12, June.
    • Handle: RePEc:plo:pone00:0234470
    DOI: 10.1371/journal.pone.0234470
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    References listed on IDEAS

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    1. Peter Edge & Vikas Bansal, 2019. "Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
    2. David Porubsky & Shilpa Garg & Ashley D. Sanders & Jan O. Korbel & Victor Guryev & Peter M. Lansdorp & Tobias Marschall, 2017. "Dense and accurate whole-chromosome haplotyping of individual genomes," Nature Communications, Nature, vol. 8(1), pages 1-10, December.
    3. Jay Shendure & Shankar Balasubramanian & George M. Church & Walter Gilbert & Jane Rogers & Jeffery A. Schloss & Robert H. Waterston, 2017. "DNA sequencing at 40: past, present and future," Nature, Nature, vol. 550(7676), pages 345-353, October.
    4. Sina Majidian & Mohammad Hossein Kahaei, 2019. "NGS based haplotype assembly using matrix completion," PLOS ONE, Public Library of Science, vol. 14(3), pages 1-12, March.
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