An overlooked phenomenon: complex interactions of potential error sources on the quality of bacterial de novo genome assemblies.

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  • Additional Information
    • Source:
      Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE
    • Publication Information:
      Original Publication: London : BioMed Central, [2000-
    • Subject Terms:
      Research Design* ; Genome, Bacterial*; Benchmarking ; High-Throughput Nucleotide Sequencing
    • Abstract:
      Background: Parameters adversely affecting the contiguity and accuracy of the assemblies from Illumina next-generation sequencing (NGS) are well described. However, past studies generally focused on their additive effects, overlooking their potential interactions possibly exacerbating one another's effects in a multiplicative manner. To investigate whether or not they act interactively on de novo genome assembly quality, we simulated sequencing data for 13 bacterial reference genomes, with varying levels of error rate, sequencing depth, PCR and optical duplicate ratios.
      Results: We assessed the quality of assemblies from the simulated sequencing data with a number of contiguity and accuracy metrics, which we used to quantify both additive and multiplicative effects of the four parameters. We found that the tested parameters are engaged in complex interactions, exerting multiplicative, rather than additive, effects on assembly quality. Also, the ratio of non-repeated regions and GC% of the original genomes can shape how the four parameters affect assembly quality.
      Conclusions: We provide a framework for consideration in future studies using de novo genome assembly of bacterial genomes, e.g. in choosing the optimal sequencing depth, balancing between its positive effect on contiguity and negative effect on accuracy due to its interaction with error rate. Furthermore, the properties of the genomes to be sequenced also should be taken into account, as they might influence the effects of error sources themselves.
      (© 2024. The Author(s).)
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    • Grant Information:
      GINOP-2.3.4-15-2020-00008 European Regional Development Fund; GINOP-2.3.4-15-2020-00008 European Regional Development Fund; GINOP-2.3.4-15-2020-00008 European Regional Development Fund; GINOP-2.3.4-15-2020-00008 European Regional Development Fund; GINOP-2.3.4-15-2020-00008 European Regional Development Fund; GINOP-2.3.4-15-2020-00008 European Regional Development Fund; GINOP-2.3.4-15-2020-00008 European Regional Development Fund
    • Contributed Indexing:
      Keywords: Bacterial genomes; Optical duplicates; PCR duplicates; Sequencing depth; Sequencing error
    • Publication Date:
      Date Created: 20240109 Date Completed: 20240111 Latest Revision: 20240112
    • Publication Date:
      20240112
    • Accession Number:
      PMC10777565
    • Accession Number:
      10.1186/s12864-023-09910-4
    • Accession Number:
      38195441