Obtaining consensus sequence from aligned sequences

Hi there, I’m trying to obtain a consensus sequence from sequences that I have already aligned.

What has been done so far is that I have uploaded multiple data obtained from PCR on galaxy. I then used Bowtie 2 to map reads against a reference genome (obtained from Genbank). I then ran ivar consensus on each of the bowtie outputs to get the consensus and aligned them on MEGA11. How do I get a single consensus from the aligned data? I tried to repeat the whole process by reuploading the aligned dataset onto galaxy and running Bowtie 2 and ivar consensus again but this gave me a sequence with alot of Ns. The aligned data set I had consists of about 30 sequences and they all aligned very well on MEGA11.

Does anyone know what I am doing wrong/what I can do to circumvent this? Thanks!

Hi @zach.low
I believe MEGA can create a consensus sequence for an alignment.
Kind regards,