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MEGARes specifications


Unique identifier OMICS_14217
Name MEGARes
Restrictions to use None
Database management system MySQL
Community driven Yes
Data access File download, Browse
User data submission Not allowed
Version 1.0.1
Maintained Yes


  • person_outline Christina Boucher

Publication for MEGARes

MEGARes citations


Impact of sequencing depth on the characterization of the microbiome and resistome

Sci Rep
PMCID: 5897366
PMID: 29651035
DOI: 10.1038/s41598-018-24280-8
call_split See protocol

[…] th Kraken’s report function. For the resistome analysis, the quality-filtered reads were provided as input to BWA-MEM alignment using default parameters including a mismatch penalty value of 4 to the MEGARes AMR genes database, without the inclusion of host genome filtering step. Reads were assigned to ARGs using a 75% gene coverage/fraction threshold. Read counts originating from alignments to ho […]


Prevalence and Genetic Basis of Antimicrobial Resistance in Non aureus Staphylococci Isolated from Canadian Dairy Herds

Front Microbiol
PMCID: 5820348
PMID: 29503642
DOI: 10.3389/fmicb.2018.00256

[…] 2349 (Naushad et al., ). Prevalence of ARGs and other resistance determinants was evaluated using data from 4 databases: (1) ARG-ANNOT v3 (Antibiotic Resistance Gene-ANNOTation) (Gupta et al., ); (2) MegaRES v1.0.1 (Lakin et al., ); (3) Comprehensive Antibiotic Resistance Database v1.1.6 (CARD) (Jia et al., ); and (4) ResFinder from the Center for Genomic Epidemiology (as of November 02, 2016) (Za […]


Establishing Genotype to Phenotype Relationships in Bacteria Causing Hospital Acquired Pneumonia: A Prelude to the Application of Clinical Metagenomics

PMCID: 5745473
PMID: 29186015
DOI: 10.3390/antibiotics6040030

[…] to detect ARGs []. Besides the Resfinder, CARD and ARG-ANNOT online search possibilities, some ARG-searching pipelines such as ARIBA (that can be run with any ARG database) [] or AMR++ (based on the MEGARes database []) that enable the detection and counts of ARGs as well as the detection of variants, have been made available. Once identified in the genomic data, an ARG is assumed to be expressed […]


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MEGARes institution(s)
Department of Clinical Sciences, Colorado State University, Fort Collins, CO, USA; Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA; Department of Computer Science, Colorado State University, Fort Collins, CO, USA; Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA; Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, USA; Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, USA
MEGARes funding source(s)
This work was supported by the Infectious Disease Supercluster and CSU Ventures at Colorado State University; Beef Checkoff; United States Department of Agriculture (2014-05257, 2015-03538) and the National Institutes of Health (5T32OD012201).

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