EVORhA (Evolutionary Reconstruction of Haplotypes) is a quasi-species assembly method that allows reconstructing from short-read sequence data of a bacterial population, the haplotypes occurring in that population and the frequencies at which they occur. EVORhA can be used amongst others to reconstruct genome-wide haplotypes obtained from a mixed bacterial infection or to reconstruct the population dynamics of an evolving bacterial population from pooled sequence data.
Frequency-based haplotype reconstruction from deep sequencing data of bacterial populations. Sergio Pulido-Tamayo, Aminael Sanchez-Rodriguez, Toon Swings, Bram Van den Bergh, Akanksha Dubey, Hans Steenackers, Jan Michiels, Jan Fostier, Kathleen Marchal. Nucl. Acids Res. (2015) doi: 10.1093/nar/gkv478