Published December 15, 2018
| Version Published + Supplemental Material
Journal Article
Open
MetaPOAP: Presence or Absence of Metabolic Pathways in Metagenome-Assembled Genomes
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1.
Harvard University
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2.
Lawrence Berkeley National Laboratory
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3.
Joint BioEnergy Institute
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4.
University of California, Davis
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5.
California Institute of Technology
Abstract
Genome-resolved metagenomics allows the construction of draft microbial genomes from short-read shotgun metagenomics (Metagenome-Assembled Genomes, or MAGs); however, even high-quality MAGs are typically somewhat incomplete and contain a small amount of contaminant sequence, making accurate prediction of metabolic potential challenging. Here, we describe MetaPOAP, an algorithm for probabalistic assessment of the statistical likelihoods for the presence or absence of metabolic pathways in MAGs.
Additional Information
© The Author(s) (2018). Published by Oxford University Press. This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/about_us/legal/notices). Received: 19 March 2018; Revision Received: 18 June 2018; Accepted: 19 June 2018; Published: 22 June 2018. Availability and implementation: MetaPOAP is available as Python scripts on GitHub or from the Fischer lab webpage, https://github.com/lmward/MetaPOAP. We thank Daan Speth and Grayson Chadwick for helpful discussion during the development of MetaPOAP. L.M.W. acknowledges support from an Agouron Institute postdoctoral fellowship. W.W.F. acknowledges support of the David and Lucile Packard Foundation and NASA Exobiology award NNX16AJ57G. P.M.S. acknowledge support from a Society in Science–Branco Weiss fellowship from ETH Zurich. Conflict of Interest: none declared.Attached Files
Published - bty510.pdf
Supplemental Material - bty510_supp.zip
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Additional details
Identifiers
- Eprint ID
- 87509
- Resolver ID
- CaltechAUTHORS:20180702-091627832
Funding
- Agouron Institute
- David and Lucile Packard Foundation
- NASA
- NNX16AJ57G
- ETH Zurich
Dates
- Created
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2018-07-03Created from EPrint's datestamp field
- Updated
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2021-11-15Created from EPrint's last_modified field