Suggestion - SILVA v132 for q2-fragment-insertion

silva
fragment-insertion

(Rachael Lappan) #1

Hello QIIME2 users and developers,

There is a discussion on preparing (and possibly benchmarking) the SILVA v132 database for use in the q2-fragment-insertion plugin.

In the current 2018.11 QIIME2 release, the SILVA database does come packaged with the plugin (for me, in miniconda2/envs/qiime2-2018.11/share/fragment-insertion/ref/) however this contains SILVA v128. I assume that many users, like me, would be using SILVA v132 and may have already done some analysis with this version of the database.

I’d like to suggest/request that the SILVA v132 database be appropriately prepared and packaged with a future release of QIIME2 so that SILVA users can utilise the q2-fragment-insertion plugin with the newest SILVA database.

I note that this may have been attempted by @ryan715b here but seems to have not been resolved/updated.

Cheers,
Rachael


(Matthew Ryan Dillon) #2

@Stefan, any thoughts about this?


(Stefan Janssen) #3

Almost a year ago, I created a pull request to enable the plugin to handle alternative references: https://github.com/qiime2/q2-fragment-insertion/pull/32
You can already provide alternative references, but SEPP will fail if the provided tree is not a subset of the existing Greengenes tree, because the raxml-info file won’t match other reference trees and currently this functionality is not exposed through the plugin. Work on this was stalled, because several lab members raised concerns about the fact that we have not benchmarked Silva for this purpose.

I have created a conda package for Silva 12.8 based on the PR https://anaconda.org/biocore/q2-fragment-insertion/2018.2.1/download/linux-64/q2-fragment-insertion-2018.2.1-py35_1.tar.bz2, but meanwhile we did some changes to the master branch and I don’t know if it is still compatible.

I’d suggest revisiting the old PR of mine and again ask Siavash to process the latest Silva 13.2 phylogeny. We then need someone to volunteer for benchmarking.


(Matthew Ryan Dillon) #4

Cool - that was long before q2-fragment-insertion was a “Core” plugin, so that PR wasn’t on our radar — we will take a look when we get a minute. Thanks!