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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.
Frontiers The efficiency of Nextera XT tagmentation depends on G
Evaluation of the sequencing depth of coverage across the three
PDF] Comparison of Sample Preparation Methods Used for the Next
PDF] Summarizing and correcting the GC content bias in high
Coverage across drug-resistance genes. The coverage across the
PDF] Summarizing and correcting the GC content bias in high
Sequencing biases of low-GC regions and assembly quality of entire
Phables: from fragmented assemblies to high-quality bacteriophage
Comparison of GC-associated sequencing biases of low-GC regions in
Phables: from fragmented assemblies to high-quality bacteriophage
The dependence of coverage on GC content. The coverage across
Predicted versus experimental coverage and percent abundance of
