Strategy for genome sequencing analysis and assembly for comparative genomics of pseudomonas genomes

Julie Jeukens, Brian Boyle, Nicholas P Tucker, Roger C Levesque

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Bacterial genome sequencing has developed rapidly in the last decade and has become a primary method for analyzing the genomic basis of differences in phenotype between strains as well as being a valuable tool for public health epidemiology. This chapter provides a comprehensive workflow for bacterial genome sequencing from experimental design to data suitable for comparative genomics analysis, while mainly focusing on the challenges associated with genome assembly. This approach was successfully applied to 19 Pseudomonas aeruginosa genomes from phenotypically distinct strains.

Original languageEnglish
Title of host publicationPseudomonas Methods and Protocols
EditorsAlain Filloux, Juan-Luis Ramos
Place of PublicationNew York
PublisherSpringer
Pages565-577
Number of pages13
ISBN (Print)9781493904730
DOIs
Publication statusPublished - 2014

Publication series

NameMethods in Molecular Biology
PublisherSpringer
Volume1149
ISSN (Print)1064-3745

Keywords

  • genome sequencing analysis
  • assembly
  • comparative genomics
  • pseudomonas genomes
  • bacterial genome
  • next-generation sequencing
  • contig
  • finishing

Cite this

Jeukens, J., Boyle, B., Tucker, N. P., & Levesque, R. C. (2014). Strategy for genome sequencing analysis and assembly for comparative genomics of pseudomonas genomes. In A. Filloux, & J-L. Ramos (Eds.), Pseudomonas Methods and Protocols (pp. 565-577). (Methods in Molecular Biology; Vol. 1149). Springer. https://doi.org/10.1007/978-1-4939-0473-0_43