A workshop for the One Health Summer Institute's Introduction to Bioinformatics sessions
- Overview of methods for bacterial genomics and molecular epidemiology
- Introduction to databases and tools for the analysis of antimicrobial resistance genes
- Introduction and overview of bioinformatics for AMR: methods and databases
- Hands-on activity with the Comprehensive Antimicrobial Resistance Database (CARD): using RGI to analyze genomes and plasmids
- Hands-on work with Galaxy: de novo ssembly of a MRSA genome and analysis of antimicrobial resistance genes
- Introduction and overview PDF slides
- Using CARD and RGI to characterize the resistome of bacterial plasmids and genomes
- Genome Assembly of MRSA using Illumina MiSeq Data (with Galaxy)
- A Primer on Infectious Disease Bacterial Genomics (Lynch et al., 2016)
- A Primer on Microbial Bioinformatics for non-bionformaticians (Carrico et al., 2018)
- Best practices for analysing microbiomes (Knight et al., 2018)