greengene version in SEPP plugin

User Support
,
1

I just have a quick question regarding to the version of greengene databse that SEPP reference tree is built on.

On this page: Greengenes 13_8 SEPP reference database, it is written as gg-13-8. But if going back to the SEPP-ref or SEPP repository, I can only find gg_13_5_ssu_align_99_pfiltered.fasta. So should we trust that the sepp file in qiime2 resources is indeeded built upon gg_13_8?

The reason I asked because I'd like to use the full length 16S sequences which were used for building the sepp tree to do some other tasks.

Thanks!

Jincheng

4

@wangj50,

gg_13_8 is follow on to gg_13_5. It uses the same alignment, which is what you are seeing. For 13_8, only the otu labels were adjusted, which has been done in SEPP/SEPP-ref. See line 70 of README.md in the SEPP-ref package for more on this.

6

Thank you! This is great to know! - Jincheng

1 Like
7

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.