Is alignment and classification possible with 16s v5-v6 region?


I have used mothur with v4 primers before, but we work in plants and would like to use v5-v6 region to remove most chloroplast.

Could we follow the same SOP regarding alignment and classification as before?



In a word, yes. The change you would need to make to the SOP is that you would need to trim the SILVA reference alignment to the V5-V6 region of the 16S gene instead of the V4 region (A how-to).

On another note, a thing to be cautious of is that if the region you are sequencing is too long so that paired reads (if using a paired read seq. tech.) do not fully overlap then you may run into other problems. The V4 region is well suited to Illumina’s 250bp pair end seq. tech. for this reason because you get fully overlapping paired reads. I don’t know the length of the V5-V6 region but just wanted to mention it in case this could be an issue for that region.


Thanks Richard :smiley: