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Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies. | LitMetric

AI Article Synopsis

  • - The study compares the performance of different sequencing platforms (Oxford Nanopore, PacBio, and Illumina) using a defined microbial community (BMock12), which includes 12 bacterial strains with varying genome sizes and characteristics.
  • - Size selection for sequencing libraries was vital to achieve similar organism abundance across all platforms, and while Illumina provided good coverage with few errors, hybrid assemblies with ONT and PacBio improved overall contiguity but led to more misassemblies in closely related genomes.
  • - The dataset generated from this research is valuable for evaluating and benchmarking bioinformatics software across the three sequencing platforms, enabling better analysis and understanding of metagenomic data.

Article Abstract

Metagenomic sequence data from defined mock communities is crucial for the assessment of sequencing platform performance and downstream analyses, including assembly, binning and taxonomic assignment. We report a comparison of shotgun metagenome sequencing and assembly metrics of a defined microbial mock community using the Oxford Nanopore Technologies (ONT) MinION, PacBio and Illumina sequencing platforms. Our synthetic microbial community BMock12 consists of 12 bacterial strains with genome sizes spanning 3.2-7.2 Mbp, 40-73% GC content, and 1.5-7.3% repeats. Size selection of both PacBio and ONT sequencing libraries prior to sequencing was essential to yield comparable relative abundances of organisms among all sequencing technologies. While the Illumina-based metagenome assembly yielded good coverage with few misassemblies, contiguity was greatly improved by both, Illumina + ONT and Illumina + PacBio hybrid assemblies but increased misassemblies, most notably in genomes with high sequence similarity to each other. Our resulting datasets allow evaluation and benchmarking of bioinformatics software on Illumina, PacBio and ONT platforms in parallel.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6879543PMC
http://dx.doi.org/10.1038/s41597-019-0287-zDOI Listing

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