Determining mutant spectra of three RNA viral samples using ultra-deep sequencing [report]

H Chen
2012 unpublished
RNA viruses have extremely high mutation rates that enable the virus to adapt to new host environments and even jump from one species to another. As part of a viral transmission study, three viral samples collected from naturally infected animals were sequenced using Illumina paired-end technology at ultra-deep coverage. In order to determine the mutant spectra within the viral quasispecies, it is critical to understand the sequencing error rates and control for false positive calls of viral
more » ... e calls of viral variants (point mutantations). I will estimate the sequencing error rate from two control sequences and characterize the mutant spectra in the natural samples with this error rate. Acknowledgement This work is part of a DTRA-funded viral evolution study headed by Monica Borucki at Lawrence Livermore National Lab. I worked closely with Jonathan Allen on bioinformatics aspects of the study. Jonathan Allen generated the nucleotide frequency distribution (.freq) files and the quality score distribution (.qscores) files, which served as the starting point of my analysis for this paper. I used two additional programs he developed in my analysis (see readme.txt).
doi:10.2172/1044235 fatcat:7ptvwnznebf2fkdf62wnrasnse