Frequency-based haplotype reconstruction from deep sequencing data of bacterial populations

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. © 2015 The Author(s).

• מחבר ראשי: Pulido-Tamayo, S. (author)
• מחברים אחרים: Dubey, A. (author), Swings, T. (author), Fostier, J. (author), Van Den Bergh, B. (author), Steenackers, H. (author), Sanchez Rodriguez, A. (author), Michiels, J. (author), Marchal, K. (author)
• פורמט: article
• יצא לאור: 2015
• גישה מקוונת: http://dspace.utpl.edu.ec/handle/123456789/18977