Thank you! I plan on giving these suggestions a try.
In the mean time I just aligned all my sequences and get the following:
Is this normal? I should note that 85% of the sequences were taxonomically assigned to genus level.
The alignment looks fine to me. There gaps result from other sequences that have insertions. They may or may not be from your target amplicon sequence, they are hyper variable regions after all. 
Most short read sequences are going to be classified to the family or genus level. Do not put too much trust in species-level assignments.
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The alignment looks fine to me. There gaps result from other sequences that have insertions. They may or may not be from your target amplicon sequence, they are hyper variable regions after all.
That is encouraging then! So it would seem the sequences are relatively normal looking, as I was concerned that somehow barcodes or primers might be left in causing the problems discussed we had previously discussed here given that they start of every sequence didn't seem to align.
For sure one should take any16S taxonomic assignment with a pinch of salt but it was just encouraging that they are being recognised as 16S sequences and not something...well different 
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