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Summary: Tychus is a tool that allows researchers to perform massively parallel whole genome sequence (WGS) analysis with the goal of producing a high confidence and comprehensive description of the bacterial genome. Key features of the Tychus pipeline include the assembly, annotation, alignment, variant discovery and phylogenetic inference of large numbers of WGS isolates in parallel using open-source bioinformatics tools and virtualization technology. All prerequisite tools and dependencies come packaged together in a single suite that can be easily downloaded and installed on Linux and Mac operating systems. Availability: Tychus is freely available as an open-source package under the MIT license, and can be down-loaded via GitHub (https://github.com/Abdo-Lab/Tychus).