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Antimicrobial resistance Genome batch analysis

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!

amr database card
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updated by Ram Ram • written by Mup123 • Mup123

Can you specify the organism?

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written by Arup Ghosh Arup Ghosh

Multiple strains of Klebsiella pneumoniae.

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written by Mup123 • Mup123

1 answer

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

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written by jv jv

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