MetaPOAP: Presence or Absence of Metabolic Pathways in Metagenome-Assembled Genomes

Creators: Ward, Lewis M.; Shih, Patrick M.; Fischer, Woodward W.

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

Files

bty510.pdf

Files (4.0 MB)

Name	Size	Download all
bty510.pdf md5:06a3808f3da45627a6c807da2517fda9	116.4 kB	Preview Download
bty510_supp.zip md5:f8b46fcaed69c9e8fe2d41ab0485adbb	3.9 MB	Preview Download

Additional details

	All versions	This version
Views	0	0
Downloads	0	0
Data volume	0 Bytes	0 Bytes