Evaluating coverage bias in next-generation sequencing of

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.

Phables: from fragmented assemblies to high-quality bacteriophage

Genotype comparison. (A) Concordance of WGS genotypes with

PDF] Illuminating Choices for Library Prep: A Comparison of

Frontiers The efficiency of Nextera XT tagmentation depends on G

Genome assembly contig count versus total length of assembly. The

Genome assembly contig count versus total length of assembly. Each

PDF) Evaluating coverage bias in next-generation sequencing of

The dependence of coverage on GC content. The coverage across

Comparison of whole genome coverage of assembled contigs mapped

Low coverage whole genome sequencing enables accurate assessment of common variants and calculation of genome-wide polygenic scores, Genome Medicine

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Frontiers Ultra Low-Coverage Whole-Genome Sequencing as an