Removing Primers and adapter

No, the actual PCR primers you used for amplification of the V3V4 region. I suspect they might be one of these two primer sets:

Region Primer Pair Name Reference Fwd primer (5' - 3') Rev primer (5' - 3')
V3V4 341F/357wF - 805R Herlemann et al. 2011 CCTACGGGNGGCWGCAG GACTACHVGGGTATCTAATCC
V3V4 341F/357wF-806R Lemons et al. 2017 CCTACGGGNGGCWGCAG GGACTACHVGGGTWTCTAAT

This is assuming the sequencing protocol used sequences through the primer, i.e. is present in the 5' region of your reads.

-Mike

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