Next generation sequencing data of a defined microbial mock community
Abstract
Generating sequence data of a defined community composed of organisms with complete reference genomes is indispensable for the benchmarking of new genome sequence analysis methods, including assembly and binning tools. Moreover the validation of new sequencing library protocols and platforms to assess critical components such as sequencing errors and biases relies on such datasets. We here report the next generation metagenomic sequence data of a defined mock community (Mock Bacteria ARchaea Community; MBARC-26), composed of 23 bacterial and 3 archaeal strains with finished genomes. These strains span 10 phyla and 14 classes, a range of GC contents, genome sizes, repeat content and encompass a diverse abundance profile. Short read Illumina and long-read PacBio SMRT sequences of this mock community are described. These data represent a valuable resource for the scientific community, enabling extensive benchmarking and comparative evaluation of bioinformatics tools without the need to simulate data. As such, these data can aid in improving our current sequence data analysis toolkit and spur interest in the development of new tools.
- Authors:
-
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Newcastle Univ. (United Kingdom)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1624549
- Alternate Identifier(s):
- OSTI ID: 1897470
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Scientific Data
- Additional Journal Information:
- Journal Volume: 3; Journal Issue: 1; Journal ID: ISSN 2052-4463
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 60 APPLIED LIFE SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; Science & technology - other topics; Next-generation sequencing; Microbial communities; DNA sequencing; Metagenomics
Citation Formats
Singer, Esther, Andreopoulos, Bill, Bowers, Robert M., Lee, Janey, Deshpande, Shweta, Chiniquy, Jennifer, Ciobanu, Doina, Klenk, Hans-Peter, Zane, Matthew, Daum, Christopher, Clum, Alicia, Cheng, Jan-Fang, Copeland, Alex, and Woyke, Tanja. Next generation sequencing data of a defined microbial mock community. United States: N. p., 2016.
Web. doi:10.1038/sdata.2016.81.
Singer, Esther, Andreopoulos, Bill, Bowers, Robert M., Lee, Janey, Deshpande, Shweta, Chiniquy, Jennifer, Ciobanu, Doina, Klenk, Hans-Peter, Zane, Matthew, Daum, Christopher, Clum, Alicia, Cheng, Jan-Fang, Copeland, Alex, & Woyke, Tanja. Next generation sequencing data of a defined microbial mock community. United States. https://doi.org/10.1038/sdata.2016.81
Singer, Esther, Andreopoulos, Bill, Bowers, Robert M., Lee, Janey, Deshpande, Shweta, Chiniquy, Jennifer, Ciobanu, Doina, Klenk, Hans-Peter, Zane, Matthew, Daum, Christopher, Clum, Alicia, Cheng, Jan-Fang, Copeland, Alex, and Woyke, Tanja. Tue .
"Next generation sequencing data of a defined microbial mock community". United States. https://doi.org/10.1038/sdata.2016.81. https://www.osti.gov/servlets/purl/1624549.
@article{osti_1624549,
title = {Next generation sequencing data of a defined microbial mock community},
author = {Singer, Esther and Andreopoulos, Bill and Bowers, Robert M. and Lee, Janey and Deshpande, Shweta and Chiniquy, Jennifer and Ciobanu, Doina and Klenk, Hans-Peter and Zane, Matthew and Daum, Christopher and Clum, Alicia and Cheng, Jan-Fang and Copeland, Alex and Woyke, Tanja},
abstractNote = {Generating sequence data of a defined community composed of organisms with complete reference genomes is indispensable for the benchmarking of new genome sequence analysis methods, including assembly and binning tools. Moreover the validation of new sequencing library protocols and platforms to assess critical components such as sequencing errors and biases relies on such datasets. We here report the next generation metagenomic sequence data of a defined mock community (Mock Bacteria ARchaea Community; MBARC-26), composed of 23 bacterial and 3 archaeal strains with finished genomes. These strains span 10 phyla and 14 classes, a range of GC contents, genome sizes, repeat content and encompass a diverse abundance profile. Short read Illumina and long-read PacBio SMRT sequences of this mock community are described. These data represent a valuable resource for the scientific community, enabling extensive benchmarking and comparative evaluation of bioinformatics tools without the need to simulate data. As such, these data can aid in improving our current sequence data analysis toolkit and spur interest in the development of new tools.},
doi = {10.1038/sdata.2016.81},
journal = {Scientific Data},
number = 1,
volume = 3,
place = {United States},
year = {Tue Sep 27 00:00:00 EDT 2016},
month = {Tue Sep 27 00:00:00 EDT 2016}
}
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Figures / Tables:
Table 1: Genome statistics of each mock community member. Genome size includes chromosomes and plasmids. All genomes are available as finished sequences. Phylum associations for each strain are abbreviated as follows: AD—Acidobacteria, AT—Actinobacteria, B—Bacteroidetes, D—Deinococcus-Thermus, E—Euryarchaeota, F—Firmicutes, P—Proteobacteria, S—Spirochaetes, T—Thermotogae, V—Verrucomicrobia. Isolation sources were obtained from literature on respective strains,more »
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