Bacterial Functional Annotation using EMU Output

[Anon1382]

Hello,

I'm quite new to bioinformatics, but I was wondering if there is an effective way to directly use the EMU output to determine the biological roles of the detected bacteria within the community.

Thanks in advance!

[kdcurry]

We do not have a recommended pipeline for this, so I will leave this up for the community to share.

However, here is one pipeline that has previously been shared: https://villapollab.github.io/covid_biome/

[AlexandreThibodeauUdM]

Hello, yes and no.

Yes, in the fact that programs such as PICRUST 2 use sequences to infere functions. So technically, you do not need to run any other pipeline to do so. This is independant from EMU.

On the other hand, if you want an exact match with EMU output and this bacteria function, you need to extract from each identified species the sequences, fetch all these sequences and remember their sequence ID and then do function analysis. Quite tedious and not recommended.

I hope it help.

Thanks for the reference. Such level of details is rare, I love to compare with what we are doing!