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Broddrick JT, Szubin R, Norsigian CJ, et al. High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies. Front Microbiol. 2020;11:596626doi: 10.3389/fmicb.2020.596626.
Broddrick, J. T., Szubin, R., Norsigian, C. J., Monk, J. M., Palsson, B. O., & Parenteau, M. N. (2020). High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies. Frontiers in microbiology, 11596626. https://doi.org/10.3389/fmicb.2020.596626
Broddrick, Jared T, et al. "High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies." Frontiers in microbiology vol. 11 (2020): 596626. doi: https://doi.org/10.3389/fmicb.2020.596626
Broddrick JT, Szubin R, Norsigian CJ, Monk JM, Palsson BO, Parenteau MN. High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies. Front Microbiol. 2020 Nov 12;11:596626. doi: 10.3389/fmicb.2020.596626. eCollection 2020. PMID: 33281796; PMCID: PMC7688782.
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Front Microbiol. 2020 Nov 12;11:596626. doi: 10.3389/fmicb.2020.596626. eCollection 2020.

High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies.

Frontiers in microbiology

Jared T Broddrick, Richard Szubin, Charles J Norsigian, Jonathan M Monk, Bernhard O Palsson, Mary N Parenteau

Affiliations

  1. Exobiology Branch, Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, CA, United States.
  2. Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.

PMID: 33281796 PMCID: PMC7688782 DOI: 10.3389/fmicb.2020.596626

Abstract

Advances in nanopore-based sequencing techniques have enabled rapid characterization of genomes and transcriptomes. An emerging application of this sequencing technology is point-of-care characterization of pathogenic bacteria. However, genome assessments alone are unable to provide a complete understanding of the pathogenic phenotype. Genome-scale metabolic reconstruction and analysis is a bottom-up Systems Biology technique that has elucidated the phenotypic nuances of antimicrobial resistant (AMR) bacteria and other human pathogens. Combining these genome-scale models (GEMs) with point-of-care nanopore sequencing is a promising strategy for combating the emerging health challenge of AMR pathogens. However, the sequencing errors inherent to the nanopore technique may negatively affect the quality, and therefore the utility, of GEMs reconstructed from nanopore assemblies. Here we describe and validate a workflow for rapid construction of GEMs from nanopore (MinION) derived assemblies. Benchmarking the pipeline against a high-quality reference GEM of

Copyright © 2020 Broddrick, Szubin, Norsigian, Monk, Palsson and Parenteau.

Keywords: MinION long-read sequencing; MinION nanopore device®; antimicrobial resistance (AMR); constraint-based model; metabolic model reconstruction; nanopore sequencing

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