Swabs to genomes: A comprehensive workflow

Madison I. Dunitz, Jenna M. Lang, Guillaume Jospin, Aaron E. Darling, Jonathan A Eisen, David A. Coil

Research output: Contribution to journalArticle

16 Citations (Scopus)

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 performit.

Original languageEnglish (US)
Article numbere960
JournalPeerJ
Volume2015
Issue number5
DOIs
StatePublished - 2015

Fingerprint

Workflow
Bioinformatics
Computational Biology
Microbial Genome
bioinformatics
Genes
Genome
Molecular biology
genome
DNA libraries
Gene Library
molecular biology
Genomics
DNA Sequence Analysis
genomics
testing
Research
sampling

Keywords

  • Bioinformatics
  • Genome assembly
  • Genome sequencing
  • Microbial genomics
  • Workflow

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)
  • Neuroscience(all)

Cite this

Dunitz, M. I., Lang, J. M., Jospin, G., Darling, A. E., Eisen, J. A., & Coil, D. A. (2015). Swabs to genomes: A comprehensive workflow. PeerJ, 2015(5), [e960]. https://doi.org/10.7717/peerj.960

Swabs to genomes : A comprehensive workflow. / Dunitz, Madison I.; Lang, Jenna M.; Jospin, Guillaume; Darling, Aaron E.; Eisen, Jonathan A; Coil, David A.

In: PeerJ, Vol. 2015, No. 5, e960, 2015.

Research output: Contribution to journalArticle

Dunitz, MI, Lang, JM, Jospin, G, Darling, AE, Eisen, JA & Coil, DA 2015, 'Swabs to genomes: A comprehensive workflow', PeerJ, vol. 2015, no. 5, e960. https://doi.org/10.7717/peerj.960
Dunitz MI, Lang JM, Jospin G, Darling AE, Eisen JA, Coil DA. Swabs to genomes: A comprehensive workflow. PeerJ. 2015;2015(5). e960. https://doi.org/10.7717/peerj.960
Dunitz, Madison I. ; Lang, Jenna M. ; Jospin, Guillaume ; Darling, Aaron E. ; Eisen, Jonathan A ; Coil, David A. / Swabs to genomes : A comprehensive workflow. In: PeerJ. 2015 ; Vol. 2015, No. 5.
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