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.
Clinical Evaluation of Metagenomic Next-Generation Sequencing and Iden
Frontiers The efficiency of Nextera XT tagmentation depends on G and C bases in the binding motif leading to uneven coverage in bacterial species with low and neutral GC-content
A framework for assessing 16S rRNA marker-gene survey data analysis methods using mixtures., Microbiome
PDF] Comparison of the sequencing bias of currently available library preparation kits for Illumina sequencing of bacterial genomes and metagenomes
Single cell sequencing - MyBioSource Learning Center
An informatic workflow for the enhanced annotation of excretory/secretory proteins of Haemonchus contortus - Computational and Structural Biotechnology Journal
Lack of genomic coverage in dfrA-thyA genes reveals deletions in the
Frontiers A Comparative Overview of Epigenomic Profiling Methods
Development of a versatile high-throughput mutagenesis assay with multiplexed short-read NGS using DNA-barcoded supF shuttle vector library amplified in E. coli
Development of a versatile high-throughput mutagenesis assay with multiplexed short-read NGS using DNA-barcoded supF shuttle vector library amplified in E. coli
Phables: from fragmented assemblies to high-quality bacteriophage genomes
Phables: from fragmented assemblies to high-quality bacteriophage genomes
Comparison of sequencing results applying different methodologies.
Long walk to genomics: History and current approaches to genome sequencing and assembly - ScienceDirect
Identifying the best PCR enzyme for library amplification in NGS
