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 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 diagnostic value of next-generation sequencing technology in sepsis

PDF] Illuminating Choices for Library Prep: A Comparison of Library Preparation Methods for Whole Genome Sequencing of Cryptococcus neoformans Using Illumina HiSeq

Genome assembly contig count versus total length of assembly. Each

Comparison of sequencing results applying different methodologies.

On the Evolution of Chromosomal Regions with High Gene Strand Bias in Bacteria

Evaluating the performance of (A) lg(RPKM), (B) genomic coverage, and

PDF] Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA.

Predicted versus experimental coverage and percent abundance of reads

Sequence bias informs k-mer bias during sequencing. Top

GC biases in NextSeq, PacBio, Nanopore, and HiSeq data. The dot plots

Clinical Evaluation of Metagenomic Next-Generation Sequencing and Iden

Marine Drugs, Free Full-Text

PDF] Summarizing and correcting the GC content bias in high-throughput sequencing

PDF] Comparison of the sequencing bias of currently available library preparation kits for Illumina sequencing of bacterial genomes and metagenomes