shotgun metagenomic data analysis

Question

[luyang1005]

Hi,

I am new to shotgun metagenomics. Currently, I got some data from shotgun metagenomics. And now I just want to know the general taxonomy of my data. Since then I can compare it with my 16S amplicon result to check the bias of the 16S data.

Is there any clue to doing this? Thanks

Answer 1

[Fabio Marroni]

I suggest you try kraken

[luyang1005]

Hi, about Kraken I have some questions. I tried Kraken today. And I found that there were several version there. Minikaren4G, karen, and ect. May I have some suggestions from you which one could be better for me. Since my current purpose is only to look at the bacteria taxonomy profiling?

[Fabio Marroni]

Kraken with standard database is a good option. There are instrcutions for the installation. If you do not have a lot of computational resources you may try minikraken.

[luyang1005]

Thanks so much. I will try to see.

[luyang1005]

Hi, May I follow up a question? I installed the kraken, and when I run the DB configure, it told me that I did not have jellyfish. However, when I download the jellyfish v1.1.11 and installed. It is interesting to find out the installed jellyfish is v2.2.3. I have tried several times. The source is right. How can I deal with this problem? Thanks.

Answer 2

[willnotburn]

You want Phylosift, developed by Jon Eisen's group at UC Davis. There's a pretty great tutorial (by an unrelated group) on it here, which also includes many other downstream analyses you may to pursue in the future.

[luyang1005]

Thanks so much. I see. I will have a try.