Metagenome Kraken MetaPhlan

Question

[bioinfo_ga]

Hi All

I am working on metagenome data using QIIME and i am able to do PICRUST analysis but as i am not getting good classification at genus ans species level i thought of shifting to kraken , centrifuge or metaphlan tools where i am getting much better resolution. But in those cases woyld it be possible to generate OTU table as i want to do picrust or picrust2 analysis.

Thanks in advance