Antimicrobial resistance Genome batch analysis

Question

[Mup123]

Hi,

If we have 100 bacterial whole genome sequences for analyzing antimicrobial resistance genes and what is the best tool to do batch analysis. (I wish to compile the results in a single heatmap)

I have checked with card (The Comprehensive Antibiotic Resistance Database), but it accepts only one sequence at a time.

Is there any commands available to solve this problem in CARD ?

Thank You!

[Arup Ghosh]

Can you specify the organism?

[Mup123]

Multiple strains of Klebsiella pneumoniae.

Answer 1

[jv]

Generally when tools are made available via a web server they aren't setup to support the execution of large batches of jobs. You can however download and install the RGI software to a computer or server that you have access to which would allow you to run your analysis in a more high-thoughput (not to mention more reproducible) fashion.

https://card.mcmaster.ca/download