Estimation of viral population structure from amplicon-based reads

Nicholas Mancuso, Alexander Artyomenko, Alex Zelikovsky, Pavel Skums, Ion Mandoiu
2013 2013 IEEE 3rd International Conference on Computational Advances in Bio and medical Sciences (ICCABS)  
Accurately estimating the structure of highly diverse viral populations is a challenging task. There are two main impediments to globally reconstructing a population. The first is the presence of sequencing errors in reads. Judiciously differentiating these errors from actual rare variants must be properly handled or the global structure may be ill-defined. Secondly, long conserved regions in the viral genome extend beyond what modern sequencers are capable of producing. As a result, the actual
more » ... result, the actual population diversity may be hidden in these targeted regions. We propose VirA, a tool for global reconstruction of a viral population that overcomes these obstacles by combining local error correction and a read-graph approach.
doi:10.1109/iccabs.2013.6629224 dblp:conf/iccabs/MancusoAZSM13 fatcat:wqvrsc64gvbwbhu2i7up4vnt2i