Introduction

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.

Publications

  1. MEGARes: an antimicrobial resistance database for high throughput sequencing.
    Cite this
    Lakin SM, Dean C, Noyes NR, Dettenwanger A, Ross AS, Doster E, Rovira P, Abdo Z, Jones KL, Ruiz J, Belk KE, Morley PS, Boucher C, 2017-01-01 - Nucleic acids research

Credits

  1. Steven M Lakin
    Developer

    Department of Clinical Sciences, Colorado State University, United States of America

  2. Chris Dean
    Developer

    Department of Microbiology, Immunology, United States of America

  3. Noelle R Noyes
    Developer

    Department of Microbiology, Immunology, United States of America

  4. Adam Dettenwanger
    Developer

    Department of Computer Science, Colorado State University, United States of America

  5. Anne Spencer Ross
    Developer

    Department of Computer Science, Colorado State University, United States of America

  6. Enrique Doster
    Developer

    Department of Clinical Sciences, Colorado State University, United States of America

  7. Pablo Rovira
    Developer

    Department of Animal Sciences, Colorado State University, United States of America

  8. Zaid Abdo
    Developer

    Department of Microbiology, Immunology, United States of America

  9. Kenneth L Jones
    Developer

    Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, United States of America

  10. Jaime Ruiz
    Developer

    Department of Computer and Information Science and Engineering, University of Florida, United States of America

  11. Keith E Belk
    Developer

    Department of Animal Sciences, Colorado State University, United States of America

  12. Paul S Morley
    Developer

    Department of Clinical Sciences, Colorado State University, United States of America

  13. Christina Boucher
    Investigator

    Department of Computer and Information Science and Engineering, University of Florida, United States of America

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Summary
AccessionBT000018
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByChristina Boucher