Kraken report or mph report to phyloseq object

Question

[valentinavan]

Hi everyone,

I have been used to work with Kaiju output files where the taxa are not hierarchically summed:

And then work with Phyloseq.

Recently, I have also used Kraken2 where the tables are differently organised.

I have also tried the flag --use-mpa-style.

I would like to make one of these outputs organised the same way as Kaiju's or find a way to transform them into a Phyloseq object.

Any other directions on how to manipulate these data (kraken, mpa) will be more than appreciated. I do not have absolutely anyone to ask in person.

Thank you

Answer 1

[medelin.ocejo]

Dear @valentinavan, I am having the same issue. Did you manage to import kraken2 output to phyloseq?