16s rRNA analysis

[bio-apple]

hi doctor, I would like to ask if there are any special processing steps required for analyzing amplicon data such as 16S V3-V4 using Kraken2, aside from the regular data quality control (e.g., removing low-quality bases and adapters), such as removing primer sequences from paired-end reads and merging the paired-end reads before inputting the results into Kraken2 for analysis?

Lu J, Salzberg S L. Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2[J]. Microbiome, 2020, 8(1): 124.