Viral quasispecies reconstruction from amplicon 454 pyrosequencing reads

Abstract

We consider the quasispecies spectrum reconstruction problem in amplicon reads. The main contribution of this paper is several methods to reconstruct HCV quasispecies from simulated error-free amplicon reads. Our comparison with existing methods for quasispecies spectrum reconstruction both based on shotgun and amplicon reads show significant advantages of the proposed technique. In most of the cases, even low coverage allows to reconstruct majority of quasispecies and very accurately estimate their frequencies in the simulated samples. The source code for all implemented algorithms is available at https://bitbucket.org/nmancuso/bioa/