ArticlePloS one2021
Evaluating coverage bias in next-generation sequencing of Escherichia coli.
Article in PloS one, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
14 citing papers in PubMed.
- Comparative metagenomic assessment of Illumina-compatible library preparation methods, short-read lengths, and PacBio HiFi sequencing reveals differences in microbial and functional diversity recovery from a complex environmental sample.Microbiology spectrum · 2026Article
- From contiguity to accuracy: Validation-centered perspectives on bacterial genome assembly.Journal of microbiology (Seoul, Korea) · 2026Review
- Comparison of whole genome sequencing approaches for Capripox viruses.BMC genomics · 2026Article
- Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient.Nature communications · 2025Article
- A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism and capacity for intra-species co-operation.PLoS biology · 2025Article
- Biases from Oxford Nanopore library preparation kits and their effects on microbiome and genome analysis.BMC genomics · 2025Article
- Assessing Bias and Reproducibility of Viral Metagenomics Methods for the Combined Detection of Faecal RNA and DNA Viruses.Viruses · 2025Article
- Preassembly Read Processing and Quality Control in Fungal Genomes, Exemplified by the Chytrid Batrachochytrium salamandrivorans.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Forensic Microbiology: When, Where and How.Microorganisms · 2024Review
- Phables: from fragmented assemblies to high-quality bacteriophage genomes.bioRxiv : the preprint server for biology · 2023Article
- Diversity of Bacterial Secondary Metabolite Biosynthetic Gene Clusters in Three Vietnamese Sponges.Marine drugs · 2022Article
- 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.Frontiers in microbiology · 2022Article
- HPV DeepSeq: An Ultra-Fast Method of NGS Data Analysis and Visualization Using Automated Workflows and a Customized Papillomavirus Database in CLC Genomics Workbench.Pathogens (Basel, Switzerland) · 2021Article
- HapAsmbl: A reference-aided pipeline for assembling haplotypes in Nanopore amplicon sequence data of polymorphic populations.Applications in plant sciencesArticle
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Registered trials
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