From Swab to Publication: Microbial Genome Sequencing Workflow
The sequencing and de novo assembly of microbial genomes has already yielded enormous scientific insight revolutionizing a diverse collection of fields, from epidemiology to ecology. In the past two decades increasing advances in DNA sequencing technology have led to the creation of a wide variety of options for DNA library preparation, sequencing and assembly. Each option comes with its own advantages and disadvantages in terms of complexity, expense, computing power, time, and experience required. The objective of the present study was to design, test, troubleshoot, and publish a comprehensive workflow for taking a researcher from a swab to a microbial genome publication; enabling even a lab with limited resources and bioinformatics experience to perform it. The workflow was designed in an attempt to democratize the process of microbial sequencing and de novo assembly, in order to make them accessible to low funded labs or even classrooms on a massive scale.