title: Swabs to genomes: a comprehensive workflow.
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.
authors.affiliation: UC Davis, Genome Center, USA.
authors.forename: Madison I
authors.initials: MI
authors.lastname: Dunitz
authors.affiliation: UC Davis, Genome Center, USA.
authors.forename: Jenna M
authors.initials: JM
authors.lastname: Lang
authors.affiliation: UC Davis, Genome Center, USA.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Jospin
authors.affiliation: ithree institute, University of Technology Sydney, Australia.
authors.forename: Aaron E
authors.initials: AE
authors.lastname: Darling
authors.affiliation: UC Davis, Genome Center, USA.
authors.forename: Jonathan A
authors.initials: JA
authors.lastname: Eisen
authors.affiliation: UC Davis, Genome Center, USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Coil
keywords: Bioinformatics; Genome assembly; Genome sequencing; Microbial genomics; Workflow