Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies
Year: 2019
Type: data-paper
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.
Source: Scientific Data
Authors: Volkan Sevim, Juna Lee, Robert Egan, Alicia Clum, Hope Hundley, Janey Lee, R. Craig Everroad, Angela M. Detweiler, Brad M. Bebout, Jennifer Pett-Ridge, Markus Göker, Alison E. Murray, Stephen R. Lindemann, Hans-Peter Klenk, Ronan O’Malley, Matthew Zane, Jan-Fang Cheng, Alex Copeland, Christopher Daum, Esther Singer, Tanja Woyke
Institutions: Joint Genome Institute, Ames Research Center, Bay Area Environmental Research Institute, Lawrence Livermore National Laboratory, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Desert Research Institute, Purdue University West Lafayette, Newcastle University, Lawrence Berkeley National Laboratory
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $1,690
Awards: G1286236842, G1356433355, G1414775356, G14554683, G1816284028, G2145270357, G2337369775, G3083819904, G3314968792, G345329420, G365575497, G3669113783, G419881185, G4248083046, G42916606, G4501827968, G498139845, G574795485, G6652958823, G7205239661, G765874931, G805243471, G8326222658, G834277795, G8948921362, G895790057, G969889393, G991281326
OpenAlex ID: W2991113705