assembly.qmd

# Genome Assembly {#sec-assembly}

The next stage of a study like this would involve genome assembly of your isolate with an assembler such as `Shovill` or `SPAdes`. However, we do not have time to conduct the assembly in this workshop, so you will be provided with a pre-assembled draft genome.

In @sec-shovill, you will assess the quality of this draft genome assembly of your study isolate `ERR531380`, visually inspecting the graph structure of the assembly, and estimating the level of completeness and contamination using the `CheckM` software.