Evaluating coverage bias in next-generation sequencing of Escherichia coli

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 th...

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Bibliographic Details
Published in:PloS one 2021-06, Vol.16 (6), p.e0253440-e0253440
Main Authors: Gunasekera, Samantha, Abraham, Sam, Stegger, Marc, Pang, Stanley, Wang, Penghao, Sahibzada, Shafi, O'Dea, Mark
Format: Article
Language:English
Subjects:
Analysis
Antimicrobial agents
Assembly
Bias
Biology and life sciences
Deoxyribonucleic acid
DNA
DNA sequencing
Drug resistance
E coli
Escherichia coli
Gene sequencing
Genetic aspects
Genomes
Infectious diseases
Laboratories
Medicine and Health Sciences
Next-generation sequencing
Physical Sciences
Research and analysis methods
Size distribution
Whole genome sequencing
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Summary: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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0253440