SILVA v128

Feature requests
1

On the 29th of september SILVA published their release 128. Even though I ran into some issues last time I tried formatting the Silva release 123 by myself (SILVA v123), I (think) I figured out which errors I made last time and gave it another go.
While all runs well (I use exactly the README file provided by prof. dr. Schloss: http://blog.mothur.org/2015/12/03/SILVA-v123-reference-files/, without any deviations this time around), again the recreated seed database is smaller than before.

 Mothur "#get.seqs(fasta=silva.nr_v128.align, taxonomy=silva.full_v128.tax, accnos=silva.seed_v128.accnos)"

Takes only 11213 sequences from my fasta/taxonomy file as opposed to 14914 for release 123. This worries me quite a bit. Especially since the seed is supposed to contain 70512 sequences (7* more!) (https://www.arb-silva.de/documentation/release-128/, under “New in Release 128”). This is apparently approx. 1300 sequences more than 123, which doesn’t correspond at all to my previous finds.
Did anyone run into the same issue?

Kind regards,

FM

2

I am aware that probably, by trimming the sequences within the primer region, we loose a bit of information but I did not expect it would be so dramatic.

3

Did you finally get to format Silva v128? Any special hint?
Thanks! :sunglasses:
JM

4

Hi Jm,

No special hints, I just tried to follow Pat’s instructions… but for the SEED I’m not really sure if I did it right.
The output and code of what I tried can be found here: http://users.ugent.be/~fpkerckh/silvav128_README.html

Good luck!

FM

5

Hi FM!

Very nice workflow! FM, thank you very much for sharing! I think it would be a good candidate to be included in the mothur wiki.

JM

6

It is already very nicely outlined on the mothur blog http://blog.mothur.org/2015/12/03/SILVA-v123-reference-files/, I just copied it from there.
I think it is just for us impatient types… :smiley:
Overall, I think that it is safer to wait until the mothur devs upload their taxonomy outline to the page of the mothur wiki, as they will make sure there are no issues with the files anymore.