#61 filtering all not microbial reads

[Sabrin Abdelghany]

Hi All,

I have metagenomic short reads from fish gill. As I am interested in the microbial community i filtered the host reads by providing a host reference. After that I did short reads classification with kraken/bracken. I am plotting the relative abundance of what is not host but I still have most reads as non microbial reads like Annelida Molluscs Arthropods. Is there is a way after i already filtered the fish host to filter everything that is not microbial reads and only keep microbial reads?

Best Regards,
Sabrin