Hi,

I am new to shotgun metagenomics analysis. However, I have used Metaphlan2, kraken, minikraken to try on my samples. The results are totally different. Especially, Metaphlan2 is different from the other two. Even kraken and minikraken differ some.

Therefore, now I do not know which result is reliable. Does anyone who has experience can give me some suggestions?

Thanks in advance.