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

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

doi:10.1007/978-1-4939-0473-0_43

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

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

Strathclyde Institute Of Pharmacy And Biomedical Sciences

Research output: Chapter in Book/Report/Conference proceeding › Chapter

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 language	English
Title of host publication	Pseudomonas Methods and Protocols
Editors	Alain Filloux, Juan-Luis Ramos
Place of Publication	New York
Publisher	Springer
Pages	565-577
Number of pages	13
ISBN (Print)	9781493904730
DOIs	https://doi.org/10.1007/978-1-4939-0473-0_43
Publication status	Published - 2014

Publication series

Name	Methods in Molecular Biology
Publisher	Springer
Volume	1149
ISSN (Print)	1064-3745

Keywords

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

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1007/978-1-4939-0473-0_43

Cite this

@inbook{0e839571bf4b498fb936d667295871b5,

title = "Strategy for genome sequencing analysis and assembly for comparative genomics of pseudomonas genomes",

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.",

keywords = "genome sequencing analysis, assembly, comparative genomics , pseudomonas genomes, bacterial genome, next-generation sequencing, contig, finishing",

author = "Julie Jeukens and Brian Boyle and Tucker, {Nicholas P} and Levesque, {Roger C}",

year = "2014",

doi = "10.1007/978-1-4939-0473-0_43",

language = "English",

isbn = "9781493904730",

series = "Methods in Molecular Biology",

publisher = "Springer",

pages = "565--577",

editor = "Filloux, {Alain } and Ramos, {Juan-Luis }",

booktitle = "Pseudomonas Methods and Protocols",

}

Strategy for genome sequencing analysis and assembly for comparative genomics of pseudomonas genomes. / Jeukens, Julie; Boyle, Brian; Tucker, Nicholas P et al.
Pseudomonas Methods and Protocols. ed. / Alain Filloux; Juan-Luis Ramos. New York: Springer, 2014. p. 565-577 (Methods in Molecular Biology; Vol. 1149).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

TY - CHAP

T1 - Strategy for genome sequencing analysis and assembly for comparative genomics of pseudomonas genomes

AU - Jeukens, Julie

AU - Boyle, Brian

AU - Tucker, Nicholas P

AU - Levesque, Roger C

PY - 2014

Y1 - 2014

N2 - 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.

AB - 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.

KW - genome sequencing analysis

KW - assembly

KW - comparative genomics

KW - pseudomonas genomes

KW - bacterial genome

KW - next-generation sequencing

KW - contig

KW - finishing

U2 - 10.1007/978-1-4939-0473-0_43

DO - 10.1007/978-1-4939-0473-0_43

M3 - Chapter

C2 - 24818933

SN - 9781493904730

T3 - Methods in Molecular Biology

SP - 565

EP - 577

BT - Pseudomonas Methods and Protocols

A2 - Filloux, Alain

A2 - Ramos, Juan-Luis

PB - Springer

CY - New York

ER -

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

Abstract

Publication series

Keywords

UN SDGs

Access to Document

Fingerprint

Cite this