Cached database with clade-specific marker genes in galaxy

[Hasuni]

Hey there,

I am currently working on a metagenomic analysis with the galaxy platform. My coworker and I recently discovered Metaphlan, and it seems to be a very powerful tool for our work. From our understanding we can just input raw sequenced data and boom out comes a comprehensive profile. Truth be told, we are are a little confused about the parameters. We were under the impression that once we upload a file into Metaphlan, in this case paired end shot gunned sequence data, that we could execute without any further uploads. This is not the case as Metaphlan prompts for a "cached database with clade-specific marker genes." Do we need to create a specific database ourselves for marker genes of interest? Does Metaphlan not already have existing databases? This is just one of things that is confusing us. It would be wonderful if we could speak to someone about Metaphlan and all of its parameters.

Hope to hear from someone soon.

Thank you,
-H

[Duy Tin Truong]

Hi Hasuni,

MetaPhlAn has a built-in database and you only need to provide it with the fastq files then it will output the species abundance profile.

You can see more information about MetaPhlAn at:

https://bitbucket.org/biobakery/metaphlan2

Thanks,

Tin

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