Journal article
Evaluating coverage bias in next-generation sequencing of Escherichia coli
PLoS ONE, Vol.16(6), Art. e0253440
2021
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.
Details
- Title
- Evaluating coverage bias in next-generation sequencing of Escherichia coli
- Authors/Creators
- S. Gunasekera (Author/Creator) - Murdoch UniversityS. Abraham (Author/Creator) - Murdoch UniversityM. Stegger (Author/Creator) - Statens Serum InstitutS. Pang (Author/Creator) - Murdoch UniversityP. Wang (Author/Creator) - Murdoch UniversityS. Sahibzada (Author/Creator) - Murdoch UniversityM. O’Dea (Author/Creator) - Murdoch University
- Publication Details
- PLoS ONE, Vol.16(6), Art. e0253440
- Publisher
- Public Library of Science
- Identifiers
- 991005541575607891
- Copyright
- © 2021 The Authors.
- Murdoch Affiliation
- Antimicrobial Resistance and Infectious Disease Laboratory
- Language
- English
- Resource Type
- Journal article
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