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Title: 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.

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [2];  [3];  [2]; ORCiD logo [4];  [5]; ORCiD logo [6]; ORCiD logo [7];  [8];  [1];  [1]; ORCiD logo [1];  [1];  [1]; ORCiD logo [9] more »; ORCiD logo [1] « less
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  2. NASA Ames Research Center, Moffett Field, CA (United States)
  3. NASA Ames Research Center, Moffett Field, CA (United States); Bay Area Environmental Research Inst., Moffett Field, CA (United States)
  4. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  5. Leibniz-Inst. DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig (Germany)
  6. Desert Research Inst., Reno, NV (United States)
  7. Purdue Univ., West Lafayette, IN (United States)
  8. Newcastle Univ., Newcastle upon Tyne (United Kingdom)
  9. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1591834
Grant/Contract Number:  
[AC02-05CH11231; AC52-07NA27344]
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Data
Additional Journal Information:
[ Journal Volume: 6; Journal Issue: 1]; Journal ID: ISSN 2052-4463
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; data acquisition; DNA sequencing; hardware and infrastructure; metagenomics

Citation Formats

Sevim, Volkan, Lee, Juna, Egan, Robert, Clum, Alicia, Hundley, Hope, Lee, Janey, Everroad, R. Craig, Detweiler, Angela M., Bebout, Brad M., Pett-Ridge, Jennifer, Göker, Markus, Murray, Alison E., Lindemann, Stephen R., Klenk, Hans-Peter, O’Malley, Ronan, Zane, Matthew, Cheng, Jan-Fang, Copeland, Alex, Daum, Christopher, Singer, Esther, and Woyke, Tanja. Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies. United States: N. p., 2019. Web. doi:10.1038/s41597-019-0287-z.
Sevim, Volkan, Lee, Juna, Egan, Robert, Clum, Alicia, Hundley, Hope, Lee, Janey, Everroad, R. Craig, Detweiler, Angela M., Bebout, Brad M., Pett-Ridge, Jennifer, Göker, Markus, Murray, Alison E., Lindemann, Stephen R., Klenk, Hans-Peter, O’Malley, Ronan, Zane, Matthew, Cheng, Jan-Fang, Copeland, Alex, Daum, Christopher, Singer, Esther, & Woyke, Tanja. Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies. United States. doi:10.1038/s41597-019-0287-z.
Sevim, Volkan, Lee, Juna, Egan, Robert, Clum, Alicia, Hundley, Hope, Lee, Janey, Everroad, R. Craig, Detweiler, Angela M., Bebout, Brad M., Pett-Ridge, Jennifer, Göker, Markus, Murray, Alison E., Lindemann, Stephen R., Klenk, Hans-Peter, O’Malley, Ronan, Zane, Matthew, Cheng, Jan-Fang, Copeland, Alex, Daum, Christopher, Singer, Esther, and Woyke, Tanja. Tue . "Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies". United States. doi:10.1038/s41597-019-0287-z. https://www.osti.gov/servlets/purl/1591834.
@article{osti_1591834,
title = {Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies},
author = {Sevim, Volkan and Lee, Juna and Egan, Robert and Clum, Alicia and Hundley, Hope and Lee, Janey and Everroad, R. Craig and Detweiler, Angela M. and Bebout, Brad M. and Pett-Ridge, Jennifer and Göker, Markus and Murray, Alison E. and Lindemann, Stephen R. and Klenk, Hans-Peter and O’Malley, Ronan and Zane, Matthew and Cheng, Jan-Fang and Copeland, Alex and Daum, Christopher and Singer, Esther and Woyke, Tanja},
abstractNote = {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.},
doi = {10.1038/s41597-019-0287-z},
journal = {Scientific Data},
number = [1],
volume = [6],
place = {United States},
year = {2019},
month = {11}
}

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