Using pre-built Kraken2 / Bracken DB

[seoldh]

Hi all,
Thanks for developing such a great tool.
I have found that the taxon i'm looking for does not exist in the Humgut based db. So I just want to use the pre-built db that kraken2 provides (Standard; https://benlangmead.github.io/aws-indexes/k2).
How do I make it compatible with phanta?

[meenachakra]

Hello and thank you for your interest in Phanta!

Question - which taxon are you interested in? We are thinking of expanding the prokaryotic portion of our DB soon to include more species, including those that are lowly prevalent in the human gut.

We could definitely help you make the standard K2 database compatible with Phanta if you wish, but please note that it does not include nearly as many viruses as MGV (please see Fig. 3B of our paper).

[seoldh]

Thank you for your reply.
I am interested in the oral and gastric fluid microbiome, which includes taxa such as T. denticola, H. pylori, etc. that are not in current Phanta DB. I had completely forgotten that MGV is integrated into the DB, and as you mentioned, using standard k2 DB doesn't seem to be a good option.
I am glad to hear that you are working on updating the DB soon. I would like to ask if you are also planning to add oral or gastric fluid microbiomes? and could you provide an estimated timeline for its release date?

[meenachakra]

Hi @seoldh , Got it, thank you for the details!
Currently we do not have plans to specifically incorporate oral and gastric fluid microbiomes; we are considering just making a version of the DB with UHGGv2 as the new prokaryotic portion. Unlike HumGut, UHGGv2 is not "filtered" on prevalence of taxa in the human gut.
UHGGv2 does contain some of the taxa you are interested in, such as H. pylori. This database should be released within a few weeks.
We may also make a more expansive DB but that would be probably in September.

[meenachakra]

If you "watch" this repo I think you can get updates on when we make changes (and you can manage the notifications in your settings).