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- person_outline Christina Boucher
Publication for MEGARes
Impact of sequencing depth on the characterization of the microbiome and resistome
[…] 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
[…] 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
[…] 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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