#Discussion
In an effort to demystify the process of microbial genome sequencing and de novo assembly, we have designed a workflow that would allow a small lab, one operating without a specialized technician or bioinformatician, to take a sample from swab to publication. There are many options for sequencing, assembling, and annotating microbial genomes. This workflow is only one path through the numerous choices that could be made in a genome sequencing project.

All of the scripts and programs for this workflow are open-source and available online for free to ensure that individual researchers and small groups are able to access and utilize the tools necessary to complete the workflow. In general, many available bioinformatic tools are free and open source, but the installation, operation and maintenance of these programs is often complex, requiring specific technical expertise or extensive detailed instructions and best practices in the field remain undefined.

Sequencing, sharing, and publishing a genome sequence can certainly be considered as an important process in its own right. Once a genome is shared other people can use that genome for various and diverse purposes. However, just because one can stop after publishing and releasing a genome sequence that does not mean one should ignore what one can do with the data. A genome sequence is also a starting point for many computational and laboratory analyses that can provide insight into evolution, ecology, physiology, biochemistry, metabolism, and more. Such analyses are beyond the scope of this workflow and paper but that should not be taken as implying they are not interesting, useful or important.