Dataset Information

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

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.

SUBMITTER: Sevim V

PROVIDER: S-EPMC6879543 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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

Sevim Volkan V Lee Juna J Egan Robert R Clum Alicia A Hundley Hope H Lee Janey J Everroad R Craig RC Detweiler Angela M AM Bebout Brad M BM Pett-Ridge Jennifer J Göker Markus M Murray Alison E AE Lindemann Stephen R SR Klenk Hans-Peter HP O'Malley Ronan R Zane Matthew M Cheng Jan-Fang JF Copeland Alex A Daum Christopher C Singer Esther E Woyke Tanja T

Scientific data 20191126 1

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 siz ...[more]

PMID: 31772173

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Dataset Information

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

Publications

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

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