State of the CARD 2019

A week of lectures, demos, and training for the Comprehensive Antibiotic Resistance Database

During McMaster Spring Mid-Term Recess (February 18-24), the McArthur lab is pleased to present a series of lectures, demonstrations, and training sessions for the Comprehensive Antibiotic Resistance Database (card.mcmaster.ca) and its associated Resistance Gene Identifier (RGI) software, sponsored by the Michael G. DeGroote Institute for Infectious Disease Research (IIDR).

Questions? Email card@mcmaster.ca

  


Workshop & Lecture material will be available herehttps://github.com/arpcard/state-of-the-card-2019


State of the CARD 2019 Lecture

Tuesday, February 19, 2 – 3 pm MDCL 2232

https://www.eventbrite.ca/e/state-of-the-card-2019-lecture-tickets-55713383229

An introductory lecture on CARD, ARO, and the RGI and their use for data harmonization, AMR surveillance & gene prevalence, genome and metagenome annotation, and their place within the national response to AMR. New efforts on AMR metagenomic analysis, virulence prediction, and identification of mobile elements will be highlighted.

Presenter: Andrew McArthur

Optional Background Reading: Jia et al. 2017. CARD 2017: expansion and model-centric curation of the Comprehensive Antibiotic Resistance Database. Nucleic Acids Research, 45, D566-573.


Web Demo of the CARD, Antibiotic Resistance Ontology (ARO), and Resistance Gene Identifier (RGI)

Tuesday, February 19, 3 – 4 pm MDCL 2232

https://www.eventbrite.ca/e/web-demo-of-the-card-aro-and-rgi-tickets-55713629967

A walkthrough of the CARD website, the Antibiotic Resistance Ontology (ARO), model- and ontological- organization of resistance sequence information, global genome surveillance, and online use of the Resistance Gene Identifier (RGI). Highly recommended if you will be attending one of the subsequent command line training sessions.

Presenter: Andrew McArthur


Hosting your own data on CARD

Wednesday, February 20, 10 – 11 am MDCL 2249

https://www.eventbrite.ca/e/hosting-your-own-data-on-card-tickets-55713736285

Do you have a collection of genome sequences and want them continuously annotated by CARD in a password-secure website? Want your sequencing pipeline to integrate with CARD or use the RGI? Join us for a discussion on how CARD can provide these services.

CARD Members: Andrew McArthur, Brian Alcock


Installing RGI on your Laptop, remote Server, or setting up an RGI server account

Wednesday, February 20, 1 – 3 pm MDCL 2249

https://www.eventbrite.ca/e/installing-rgi-tickets-55713826555

Want to run your own RGI analysis? Need to use options not supported on the CARD website? Want to analyze your metagenomics data? Attend this session to get RGI up and running on your laptop or server or alternatively get registered and started with a RGI server account.

CARD Members: Amos Raphenya, Brian Alcock, Andrew McArthur

Requires familiarity with the command line.


Command Line RGI for genomes & genome assemblies: resistome annotation and visualization

Thursday, February 21, 10 am – 12 pm MDCL 2247

https://www.eventbrite.ca/e/command-line-rgi-for-genomes-tickets-55713945912

A training session on how to analyze genomes, genome assemblies, or metagenomic assemblies using RGI at the command line, plus an introduction to publication grade heat map generation.

CARD Members: Amos Raphenya, Brian Alcock, Andrew McArthur

Requires RGI installed on your laptop or remote server or a RGI server account. Requires familiarity with the command line.


Command Line RGI for metagenomics & pathogen-of-origin prediction

Thursday, February 21, 2 – 4 pm MDCL 3410

https://www.eventbrite.ca/e/command-line-rgi-for-metagenomics-tickets-55714013113

A training session on CARD’s latest software tools (beta testing) for analysis of metagenomic reads, including an overview of the Burrows Wheeler Transform, the importance of diverse reference sequences, and k-mer algorithms for prediction of pathogen-of-origin of AMR genes.

CARD Members: Amos Raphenya, Brian Alcock, Andrew McArthur

Requires RGI installed on your laptop or remote server or a RGI server account. Requires familiarity with the command line.


Drop-In Session

Visit us in the lab with your questions. No sign up required.

Friday, February 22, 9 am – 4 pm, MDCL 2317

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