# q2-fragment-insertion with silva v138
**URL:** https://forum.qiime2.org/t/q2-fragment-insertion-with-silva-v138/17581
**Category:** Silva
**Tags:** silva, fragment-insertion
**Created:** [November 24, 2020, 9:40pm UTC](https://forum.qiime2.org/t/q2-fragment-insertion-with-silva-v138/17581 "2020-11-24T21:40:15Z")
**Posts on this page:** 4
**Page:** 1
### Author:  [@hsapers](https://forum.qiime2.org/u/hsapers)
#### Post date: [November 24, 2020, 9:40pm UTC](https://forum.qiime2.org/t/q2-fragment-insertion-with-silva-v138/17581/1 "2020-11-24T21:40:16Z")
Hello,
Thanks for all of the support on these forums. I'm working on creating a [fragment insertion tree](https://library.qiime2.org/plugins/q2-fragment-insertion/16/) 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](https://msystems.asm.org/content/3/3/e00021-18) and looked through a few forum posts ([SILVA v132 for q2-fragment-insertion](https://forum.qiime2.org/t/suggestion-silva-v132-for-q2-fragment-insertion/7844), 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](https://github.com/smirarab/sepp-refs/tree/master/silva) but with SILVA v138? There seems to be some discussion that this is [not straight forward](https://forum.qiime2.org/t/q2-fragment-insertion-reference-info/4360). 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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### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [November 25, 2020, 6:49am UTC](https://forum.qiime2.org/t/q2-fragment-insertion-with-silva-v138/17581/2 "2020-11-25T06:49:43Z")
Hi @hsapers!
There has been some (long) discussion about how to build a SILVA 138 reference tree here:
> [@Trouble generating SeppReferenceDatabase qza](https://forum.qiime2.org/t/trouble-generating-seppreferencedatabase-qza/16729):
>
> Hi! I'm new to qiime2, so I'm not sure if I'm having problems because I couldn't find instructions for importing/creating a SeppReferenceDatabase. Goal: Use a customized subset of Silva 138 NR99 for sepp fragment insertion. What I've done: Using arb, exported the aligned fasta for the high quality seqs I want to use, after trimming to just the relevant 16S region, and exported the corresponding tree. Followed [Siavash's steps](https://github.com/smirarab/sepp-refs/tree/master/silva) to clean up the tree, resolve polytomies, and re-estimate branch …
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).
> [@hsapers](#):
>
> I’m assuming that the reference tree should be calculated using the full length reference sequences and not just the targeted amplicon region?
Yes! definitely... using the full-length sequences for a more reliable phylogeny is the goal here.
> [@hsapers](#):
>
> Apologies if I’ve missed something straight forward.
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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### Author:  [@hsapers](https://forum.qiime2.org/u/hsapers)
#### Post date: [December 7, 2020, 3:50pm UTC](https://forum.qiime2.org/t/q2-fragment-insertion-with-silva-v138/17581/6 "2020-12-07T15:50:56Z")
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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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [January 8, 2021, 1:24am UTC](https://forum.qiime2.org/t/q2-fragment-insertion-with-silva-v138/17581/8 "2021-01-08T01:24:42Z")
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