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Inferring Viral Quasispecies Spectra From 454 Pyrosequencing Reads, Irina Astrovskaya, Bassam Tork, Serghei Mangul, Kelly Westbrooks, Ion Măndoiu, Peter Balfe, Alexander Zelikovskiy
Inferring Viral Quasispecies Spectra From 454 Pyrosequencing Reads, Irina Astrovskaya, Bassam Tork, Serghei Mangul, Kelly Westbrooks, Ion Măndoiu, Peter Balfe, Alexander Zelikovskiy
Computer Science Faculty Publications
Background: RNA viruses infecting a host usually exist as a set of closely related sequences, referred to as quasispecies. The genomic diversity of viral quasispecies is a subject of great interest, particularly for chronic infections, since it can lead to resistance to existing therapies. High-throughput sequencing is a promising approach to characterizing viral diversity, but unfortunately standard assembly software was originally designed for single genome assembly and cannot be used to simultaneously assemble and estimate the abundance of multiple closely related quasispecies sequences.
Results: In this paper, we introduce a new Viral Spectrum Assembler (ViSpA) method for quasispecies spectrum reconstruction …