title: MEGARes: an antimicrobial resistance database for high throughput sequencing.
abstract: Antimicrobial resistance has become an imminent concern for public health. As methods for detection and characterization of antimicrobial resistance move from targeted culture and polymerase chain reaction to high throughput metagenomics, appropriate resources for the analysis of large-scale data are required. Currently, antimicrobial resistance databases are tailored to smaller-scale, functional profiling of genes using highly descriptive annotations. Such characteristics do not facilitate the analysis of large-scale, ecological sequence datasets such as those produced with the use of metagenomics for surveillance. In order to overcome these limitations, we present MEGARes (https://megares.meglab.org), a hand-curated antimicrobial resistance database and annotation structure that provides a foundation for the development of high throughput acyclical classifiers and hierarchical statistical analysis of big data. MEGARes can be browsed as a stand-alone resource through the website or can be easily integrated into sequence analysis pipelines through download. Also via the website, we provide documentation for AmrPlusPlus, a user-friendly Galaxy pipeline for the analysis of high throughput sequencing data that is pre-packaged for use with the MEGARes database.
authors.affiliation: Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523, USA.
authors.forename: Steven M
authors.initials: SM
authors.lastname: Lakin
authors.affiliation: Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
authors.forename: Chris
authors.initials: C
authors.lastname: Dean
authors.affiliation: Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
authors.forename: Noelle R
authors.initials: NR
authors.lastname: Noyes
authors.affiliation: Department of Computer Science, Colorado State University, Fort Collins, CO 80523, USA.
authors.forename: Adam
authors.initials: A
authors.lastname: Dettenwanger
authors.affiliation: Department of Computer Science, Colorado State University, Fort Collins, CO 80523, USA.
authors.forename: Anne Spencer
authors.initials: AS
authors.lastname: Ross
authors.affiliation: Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523, USA.
authors.forename: Enrique
authors.initials: E
authors.lastname: Doster
authors.affiliation: Department of Animal Sciences, Colorado State University, Fort Collins, CO 80523, USA.
authors.forename: Pablo
authors.initials: P
authors.lastname: Rovira
authors.affiliation: Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
authors.forename: Zaid
authors.initials: Z
authors.lastname: Abdo
authors.affiliation: Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA.
authors.forename: Kenneth L
authors.initials: KL
authors.lastname: Jones
authors.affiliation: Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611, USA.
authors.forename: Jaime
authors.initials: J
authors.lastname: Ruiz
authors.affiliation: Department of Animal Sciences, Colorado State University, Fort Collins, CO 80523, USA.
authors.forename: Keith E
authors.initials: KE
authors.lastname: Belk
authors.affiliation: Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523, USA.
authors.forename: Paul S
authors.initials: PS
authors.lastname: Morley
authors.affiliation: Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611, USA cboucher@cise.ufl.edu.
authors.forename: Christina
authors.initials: C
authors.lastname: Boucher
mesh_terms: D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D004352:Drug Resistance, Microbial; D059014:High-Throughput Nucleotide Sequencing; D054892:Metagenome; D056186:Metagenomics / Q000379:methods; D064878:Web Browser