MEGARes: an antimicrobial resistance database for high throughput sequencing

Lakin S, Dean C, Noyes NR*, Dettenwanger A, Ross A, Doster E, Rovira P, Abdo Z, Jones K, Ruiz J, Belk KE, Morley PS, Boucher C

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

Steven Lakin
Chris Dean
Noelle Noyes
Enrique Doster
Pablo Rovira
Zaid Abdo
Kenneth Jones
Jaime Ruiz
Keith Belk
Paul Morley
Christina Boucher

Citation

Lakin S*, Dean C*, Noyes NR*, Dettenwanger A, Ross A, Doster E, Rovira P, Abdo Z, Jones K, Ruiz J, Belk KE, Morley PS, Boucher C. MEGARes: an antimicrobial resistance database for high throughput sequencing. Nucleic Acid Res 2016 epub [doi: 10.1093/nar/gkw1009]. *authors contributed equally.