Question

Antimicrobial resistance Genome batch analysis

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2.3 years ago

Mup123 • 0

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 • 960 views

ADD COMMENT • link updated 2.1 years ago by Ram 44k • written 2.3 years ago by Mup123 • 0

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Can you specify the organism?

ADD REPLY • link 2.3 years ago by Arup Ghosh 3.2k

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Multiple strains of Klebsiella pneumoniae.

ADD REPLY • link 2.3 years ago by Mup123 • 0

score 1 · Answer 1 · 2022-08-23

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