q2-fragment-insertion with silva v138

Thanks for all of the support on these forums. I’m working on creating a fragment insertion tree but would like to use the SILVA 138 database as a reference. I’m not clear on the format of the reference database. I’ve had a look at the fragment-insertion paper and looked through a few forum posts (SILVA v132 for q2-fragment-insertion, and the threads linked therein) but I was having trouble following the status of the discussions. To create a reference tree for fragment insertion, can I follow the directions here but with SILVA v138? There seems to be some discussion that this is not straight forward. I’m assuming that the reference tree should be calculated using the full length reference sequences and not just the targeted amplicon region? Apologies if I’ve missed something straight forward. Thanks

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Hi @hsapers!

There has been some (long) discussion about how to build a SILVA 138 reference tree here:

The last post in that topic links to the instructions for building a reference tree (looks like the same steps that you linked to, plus a few additional steps).

Yes! definitely… using the full-length sequences for a more reliable phylogeny is the goal here.

Not at all… this is something that should probably be added to q2-fragment-insertion or another plugin at some point… up until now the reference phylogenies have mostly been built and distributed by others, but it would be ideal to democratize this process.

Good luck!

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Thank you @Nicholas_Bokulich

I’m working with the Silva v128 reference right now. But will I be upgrading and making some new reference databases with the v138 release and some in-house data - this will come in handy in the near future

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