Murdoch University Research Repository

Welcome to the Murdoch University Research Repository

The Murdoch University Research Repository is an open access digital collection of research
created by Murdoch University staff, researchers and postgraduate students.

Learn more

Evaluating coverage bias in next-generation sequencing of Escherichia coli

Gunasekera, S., Abraham, S., Stegger, M., Pang, S., Wang, P., Sahibzada, S.ORCID: 0000-0001-7362-8323 and O’Dea, M.ORCID: 0000-0002-2757-7585 (2021) Evaluating coverage bias in next-generation sequencing of Escherichia coli. PLoS ONE, 16 (6). Art. e0253440.

[img]
Preview
PDF - Published Version
Download (1MB) | Preview
Free to read: https://doi.org/10.1371/journal.pone.0253440
*No subscription required

Abstract

Whole-genome sequencing is essential to many facets of infectious disease research. However, technical limitations such as bias in coverage and tagmentation, and difficulties characterising genomic regions with extreme GC content have created significant obstacles in its use. Illumina has claimed that the recently released DNA Prep library preparation kit, formerly known as Nextera Flex, overcomes some of these limitations. This study aimed to assess bias in coverage, tagmentation, GC content, average fragment size distribution, and de novo assembly quality using both the Nextera XT and DNA Prep kits from Illumina. When performing whole-genome sequencing on Escherichia coli and where coverage bias is the main concern, the DNA Prep kit may provide higher quality results; though de novo assembly quality, tagmentation bias and GC content related bias are unlikely to improve. Based on these results, laboratories with existing workflows based on Nextera XT would see minor benefits in transitioning to the DNA Prep kit if they were primarily studying organisms with neutral GC content.

Item Type: Journal Article
Murdoch Affiliation(s): Antimicrobial Resistance and Infectious Disease Laboratory
Publisher: Public Library of Science
Copyright: © 2021 The Authors.
URI: http://researchrepository.murdoch.edu.au/id/eprint/61400
Item Control Page Item Control Page

Downloads

Downloads per month over past year