Abstract
The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become much easier for research labs with access to standard molecular biology and computational tools. However, there are a confusing variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.
Highlights
Thanks to decreases in cost and difficulty, sequencing the genome of a microorganism is becoming a relatively common activity in many research and educational institutions
As part of this project, undergraduate students isolated and classified microbes, sequenced and assembled their genomes, submitted the genome sequences to databases housed by The National Center for Biotechnology Information (NCBI), and published the genomes (Lo et al, 2013; Bendiks et al, 2013; How to cite this article Dunitz et al (2015), Swabs to genomes: a comprehensive workflow
We describe an approach to genome sequencing that allows a researcher to go from a swab to a published paper (Fig. 1)
Summary
Thanks to decreases in cost and difficulty, sequencing the genome of a microorganism is becoming a relatively common activity in many research and educational institutions. The project focused on the Built Environment because it was part of the larger “microBEnet” (microbiology of the Built Environment network, www.microbe.net) effort This project serves many purposes, including (1) engaging undergraduates in research on microbiology of the Built Environment, (2) generating “reference genomes” for microbes that are found in the Built Environment, and (3) providing a resource for educational activities on the microbiology of the Built Environment. It is possible to carry out many of the computational parts of this workflow in a Windows environment but getting these steps to work in Windows is outside the scope of this project Some parts of this workflow require the user to provide text instructions for software programs by using a command line interface. To access the command line on a Mac open the Terminal program (the default location for this program is in the “Utilities” folder under “Applications”) When this application is launched, a new window will appear. We will walk you through how to run all of the programs required for this workflow, but you must first acquire a basic familiarity
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