Viral Genome Assembler (VGA) is a method for accurate assembly of a heterogeneous viral population consisting of individuals viral genomes (also known as quasi-species). VGA is coupled with a high-fidelity sequencing protocol able to eliminate errors from sequencing data. Deep coverage in combination with highly accurate data allows VGA to accurately estimate the underlying diversity of a viral population. VGA is the first viral assembly method that scales to millions of paired-end sequencing reads. The ability of our method to maintain high assembly accuracy makes it suitable for clinical applications.

VGA was created by Serghei Mangul, Nicholas C. Wu, Nicholas Mancuso, Alex Zelikovsky, Ren Sun and Eleazar Eskin

VGA source code

The open source C/Python implementation of VGA is freely available for download.


S. Mangul, N. Wu, N. Mancuso, A. Zelikovsky, R. Sun and E. Eskin, “Accurate viral population assembly from ultra-deep sequencing data”, 17th Annual International Conference on Research in Computational Molecular Biology (ISMB 2014), Read more


For general questions, comments or suggestions about VGA, please email Serghei Mangul (serghei (AT)