Data Processing of Escherichia coli Genome Sequencing, Characterization, and Comparison
Gian Marco Baranzoni, Erin R. Reichenberger and David S. Needleman
from: Pathogenic Escherichia coli: Evolution, Omics, Detection and Control (Edited by: Pina M. Fratamico, Yanhong Liu and Christopher H. Sommers). Caister Academic Press, U.K. (2018) Pages: 143-184.
Pathogenic Escherichia coli continue to raise concerns as one of the major causes of foodborne diseases, bloodstream infections, and urinary tract infections. The remarkable advances in DNA sequencing technologies offer new alternative approaches for detection, characterisation, and tracking of pathogenic E. coli strains with higher resolution and rapid analysis time. This chapter focuses on the main steps for analysing whole-genome sequencing data and includes tools and databases suitable for E. coli genome analysis by scientists with programming and non-programming backgrounds. In particular, different sequencing platforms, typical input/output file formats, and raw data inspection and quality control assessment strategies are reviewed. Also discussed are de novo genome assembly, draft assembly improvement, and assembly visualization, as well as E. coli predictive genomic tools for serotyping and detection of virulence genes, antimicrobial resistance genes, and mobile genetic elements. Examples of genetic content comparisons and pan-genome characterisation and phylogeny are provided read more ...