Introduction

Clonal populations accumulate mutations over time, resulting in different haplotypes. Deep sequencing of such a population in principle provides information to reconstruct these haplotypes and the frequency at which the haplotypes occur. However, this reconstruction is technically not trivial, especially not in clonal systems with a relatively low mutation frequency. The low number of segregating sites in those systems adds ambiguity to the haplotype phasing and thus obviates the reconstruction of genome-wide haplotypes based on sequence overlap information.Therefore, we present EVORhA, a haplotype reconstruction method that complements phasing information in the non-empty read overlap with the frequency estimations of inferred local haplotypes. As was shown with simulated data, as soon as read lengths and/or mutation rates become restrictive for state-of-the-art methods, the use of this additional frequency information allows EVORhA to still reliably reconstruct genome-wide haplotypes. On real data, we show the applicability of the method in reconstructing the population composition of evolved bacterial populations and in decomposing mixed bacterial infections from clinical samples.

Publications

  1. Frequency-based haplotype reconstruction from deep sequencing data of bacterial populations.
    Cite this
    Pulido-Tamayo S, Sánchez-Rodríguez A, Swings T, Van den Bergh B, Dubey A, Steenackers H, Michiels J, Fostier J, Marchal K, 2015-09-01 - Nucleic acids research

Credits

  1. Sergio Pulido-Tamayo
    Developer

    Department of Information Technology, Ghent University, Belgium

  2. Aminael Sánchez-Rodríguez
    Developer

    Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, Belgium

  3. Toon Swings
    Developer

    Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, Belgium

  4. Bram Van den Bergh
    Developer

    Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, Belgium

  5. Akanksha Dubey
    Developer

    Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, Belgium

  6. Hans Steenackers
    Developer

    Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, Belgium

  7. Jan Michiels
    Developer

    Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, Belgium

  8. Jan Fostier
    Developer

    Department of Information Technology, Ghent University, Belgium

  9. Kathleen Marchal
    Investigator

    Department of Information Technology, Ghent University, Belgium

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Summary
AccessionBT006330
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionBelgium
Submitted ByKathleen Marchal