Greengenes2 alignment and analysis

Commands in mothur
1

Hi!

I am trying to use green genes 2 as my database for assigning 16s sequences. I saw that there is a greengenes reference alignment available in the SOP. Would this reference be sufficient for alignment and then I can use green genes 2 database for analysis?

I tried using green genes 2 as a reference for allignment and get this error:

mothur > align.seqs(fasta=CL1.trim.unique.fasta, reference=greengenes2.fasta

Reading in the greengenes2.fasta template sequences… [ERROR]: template is not aligned, aborting.
DONE.
It took 0 to read 0 sequences.

2

Hi there!

The only reference alignment that I recommend is the SILVA reference alignment with align.seqs. The greengenes2 reference is not aligned and is only appropriate for classification purposes with classify.seqs. Of course, you can also use the SILVA and RDP references for classification too.

pat

3

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