Using Silva v119 in align.seqs and classify.seqs

Commands in mothur
1

I see the new Silva database that is now available on the wiki. I have read the ‘readme’ file. But I’m still confused.
Normally I run align.seqs as such:
align.seqs(fasta=Pigs4to6.shhh.trim.unique.fasta, reference=silva.all.Dec2012.fasta, flip=t)
Where silva.all.Dec2012.fasta is the merged file for the last release (Dec2012 simply because that was the month I merged files).

Can silva.nr_v119.align now be used as the alignment file as reference=silva.nr_v119.align?

And then, how does this all combine with a nogap file when I go to run classify.seqs? Previously I had used:
template=nogap.all.Dec2012.fasta, taxonomy=silva.all.silva.Dec2012.tax
I think I understand that I’d use silva.nr_v119.tax here, but what about the template file?

Thanks.

2

Can silva.nr_v119.align now be used as the alignment file as reference=silva.nr_v119.align?

Yes!

And then, how does this all combine with a nogap file when I go to run classify.seqs? Previously I had used:
template=nogap.all.Dec2012.fasta, taxonomy=silva.all.silva.Dec2012.tax
I think I understand that I’d use silva.nr_v119.tax here, but what about the template file?

So actually all the nogap stuff was unnecessary. mothur automatically removes the gaps from the reference/template file for you. So the fasta and tax files are all you need.

Pat

3

Thanks for you help!