q2-shogun and q2-metaphlan2 plugins


I have used Qiime2 for 16S metagenomics. Nonetheless, now I started to perform shotgun.

To classify my metagenomic reads at taxonomic levels I used three different software: Kraken2, MetaPhlan3 and Kaiju.

I would like to create the phyloseq object including a phylogenetic tree in order to perform Unifrac distance analysis.

However, I do not know how to construct phylogenic trees from my classifiers output (from Kraken2, MetaPhlan3 and Kaiju).

1 ) I would like to ask if the qiime plugins q2-shogun and q2-metaphlan2 could help me to construct a phylogenic tree that after I can include in the phyloseq object.

2 ) Also, to classify in Kraken2... I used the following databases: proGenomes, UHGG and Metaphlan database. I do not know if I can include this genomes from these databases in q2-shogun?

  1. One plausible strategy for q2-shogun would be downloading all the reference genomes of the databases used that were match in taxonomy classifier (eg. Kraken2), and perform bowtie index for all those genomes downloaded?

thanks on advance for your help/hints,


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Hello and welcome to the forum!
Tree for metaphlan3 can be obtained from their github repository. Here is a direct link.

Since I am able to answer only one aspect of your question, I will leave it queued for other mods.


Thanks @timanix.

Yes, metaphlan, as far as I know, is the only software tool from three selected that facilitates the tree. Thanks.

Thank you for your quick response and I will attend for some ideas/hints from Kraken2 and Kaiju and their plausible use in q2-shogun.


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Hi @magibc and @timanix ,

For what its worth, I use kraken2 with the GTDB database and then use the GTDB tree. I like GTDB because the experience is closer to an OTU table (i.e. represented in counts) verses metaphlan which requires more manipulation to get into counts. The downside is that the GTDB database is large and the taxonomic names have changed slightly in new and interesting ways.



Hi Justine @jwdebelius,

Yes, it's true that in GTDB database there is available an archea and bacteria tree in Newick format. Thank you for your recommendation. I will compare the genome dataset between GTDB and UHGG for checking similitudes, and then I could think if re-run Kraken2 + Bracken using GTDB database.

Thank you,


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