Using SWIFT 16SITS and Qiaseq 16S kits it's possible to target all 16S rRNA gene. However how can i split this gene in 9 hypervariables regions V1V2, V2V3, V3V4, V4V5, V5V6, V6v7, V7V8, V8V9 because i want to investigate each region individually ? Moreover, for QIASEQ and Swift i don't have the sequences of the primers used for this purpose since they supply a pool of primers with unknown sequences. i find this article Development of an Analysis Pipeline Characterizing Multiple Hypervariable Regions of 16S rRNA Using Mock Samples
Referring to table 1 indicated in the article and qiime2 which command shall i use to align the reads to silva reference database and how can i set the start stop coordinates as indicated in table 1 to split the reads ?