U.S. Department of EnergyOffice of Scientific and Technical Information
Genome Extraction from Shotgun Metagenome Sequence Data
Abstract
Uncultivated Bacteria and Archaea comprise the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only recently become possible. To realize the hope of capturing Earth’s microbial genetic complement, technologies that accelerate recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAG genomes, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq, and others. While portions of such capabilities are individually available from other resources, the combination of the intuitive usability, data interoperability, and integration of tools in a freely available compute resource makes KBase a uniquely powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended, with additional MAG recovery and analysis tools, viamore »
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- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Accelerator & Fusion Research Division
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Argonne National Lab. (ANL), Argonne, IL (United States)
- Publication Date:
- Research Org.:
- U.S. Department of Energy Systems Biology Knowledgebase
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1831502
- DOI:
- https://doi.org/10.25982/33233.606/1831502
Citation Formats
Chivian, Dylan, Jungbluth, Sean P, Dehal, Paramvir S, Canon, Richard S, Allen, Benjamin H, Clark, Mikayla M, Gu, Tianhao, Land, Miriam L, Price, Gavin A, Riehl, William J, Sneddon, Michael W, Sutormin, Roman, Zhang, Qizhi, Cottingham, Robert W, Henry, Christopher S, and Arkin, Adam P. Genome Extraction from Shotgun Metagenome Sequence Data. United States: N. p., 2021.
Web. doi:10.25982/33233.606/1831502.
Chivian, Dylan, Jungbluth, Sean P, Dehal, Paramvir S, Canon, Richard S, Allen, Benjamin H, Clark, Mikayla M, Gu, Tianhao, Land, Miriam L, Price, Gavin A, Riehl, William J, Sneddon, Michael W, Sutormin, Roman, Zhang, Qizhi, Cottingham, Robert W, Henry, Christopher S, & Arkin, Adam P. Genome Extraction from Shotgun Metagenome Sequence Data. United States. doi:https://doi.org/10.25982/33233.606/1831502
Chivian, Dylan, Jungbluth, Sean P, Dehal, Paramvir S, Canon, Richard S, Allen, Benjamin H, Clark, Mikayla M, Gu, Tianhao, Land, Miriam L, Price, Gavin A, Riehl, William J, Sneddon, Michael W, Sutormin, Roman, Zhang, Qizhi, Cottingham, Robert W, Henry, Christopher S, and Arkin, Adam P. 2021.
"Genome Extraction from Shotgun Metagenome Sequence Data". United States. doi:https://doi.org/10.25982/33233.606/1831502. https://www.osti.gov/servlets/purl/1831502. Pub date:Mon Nov 08 23:00:00 EST 2021
@article{osti_1831502,
title = {Genome Extraction from Shotgun Metagenome Sequence Data},
author = {Chivian, Dylan and Jungbluth, Sean P and Dehal, Paramvir S and Canon, Richard S and Allen, Benjamin H and Clark, Mikayla M and Gu, Tianhao and Land, Miriam L and Price, Gavin A and Riehl, William J and Sneddon, Michael W and Sutormin, Roman and Zhang, Qizhi and Cottingham, Robert W and Henry, Christopher S and Arkin, Adam P},
abstractNote = {Uncultivated Bacteria and Archaea comprise the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only recently become possible. To realize the hope of capturing Earth’s microbial genetic complement, technologies that accelerate recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAG genomes, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq, and others. While portions of such capabilities are individually available from other resources, the combination of the intuitive usability, data interoperability, and integration of tools in a freely available compute resource makes KBase a uniquely powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended, with additional MAG recovery and analysis tools, via the KBase SDK (Software Development Kit).},
doi = {10.25982/33233.606/1831502},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Mon Nov 08 23:00:00 EST 2021},
month = {Mon Nov 08 23:00:00 EST 2021}
}