Next Generation Sequencing (NGS) is a powerful technology that has enabled sequencing of thousands to millions of DNA molecules simultaneously. NGS can be applied to any species and source of DNA including viral genomes. CliqueSNV is a novel reference-based tool for reconstruction of viral variants from NGS data. In this thesis, we present a graphical user interface for CliqueSNV installed on Galaxy and as a standalone application such that microbiologists can use the tool without having to type any command line instructions and can also run multiple experiments and include it into pipelines.