Virus

Inference of viral quasispecies with a paired de Bruijn graph

4 monthes ago   |   By Oxford Journals

AbstractMotivationRNA viruses exhibit a high mutation rate and thus they exist in infected cells as a population of closely related strains called viral quasispecies. The viral quasispecies assembly problem asks to characterise the quasispecies present in a sample from high-throughput sequencing data. We study the de novo version of the problem, where reference sequences of the quasispecies are not available. Current methods for assembling viral quasispecies are either based on overlap graphs or on de Bruijn graphs. Overlap graph based methods tend to be accurate but slow, whereas de...
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