qiime fragment-insertion sepp Silva 18S

[Manuela_Ramalho]

Hello everyone,

I would love to use the SEPP with the 18S library. But I’m in doubt if I use the file “sepp-refs-silva-128.qza” (available here https://github.com/qiime2/docs/blob/master/source/data-resources.rst) is the reference correct database. Does anyone have any tips or suggestions?

Thank you very much in advance!

All the best,
Manu

[Nicholas_Bokulich]

Hi @Manuela_Ramalho,
The link on the data-resources page leads here, where the process used to make the base files is described. It looks like the full SILVA 128 release SSU was used to generate that file, so I believe that this would be appropriate for 18S work. However, the best way to make sure would be (1) inspect the reference file, (2) just try running it to see what happens, (3) build your own reference following the instructions at that link.

Good luck!