Use of Kraken output for functional analysis

Question

[Srinka]

Is there anyone available to assist me in utilizing Kraken output for functional analysis? I've been on the lookout for tools capable of processing Kraken report output for functional analysis.

[dthorbur]

You're going to have to be more specific. "Functional analysis" is a catchall for a lot of different types of possible downstream analyses. Finding recent studies that have similar data is a good place to start in finding appropriate tools.

[Srinka]

Hi, by functional analysis I meant the pathways the microbes are involved in.

[gv]

Hello,

You can convert your classified Kraken report to the BIOM format, and then use the PICRUSt tool to predict the functions associated with KEGG and COG based on the OTU information present in the samples.

Thanks!

[Srinka]

Hello, Thanks for your suggestion. I will surely try this.

[Srinka]

Can you please suggest any tool to help convert the Kraken report to BIOM format?

[gv]

Hello,

you can use kraken-biom [kraken_biom.py] tool to get your Biom file from input kreport

cheers,