Hello Qiime2 users,
I wrote a small program that trims off the Heterogeneity Spacer (HS) bases before the primer in the reads. This trimmer removes the HS bases, keeps the primer on the reads and discardes any reads with no primers attached.
Here is the link on Github: https://github.com/noushing/Trimming_HS_Metagenomics
Let me know if you have any questions/comments.