I am processing multi-amplicon sequencing data from Ion GS S5 sequencing platform. My basic approach involves DADA2 denoising followed by feature classification using classify-consensus-blast/vsearch.
After classification, I am getting partial taxonomic assignment ( till family level/ class level) eg- "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;;;__" .
I understand this might be happening due to poor primer trimming/small amplicon length or some other reason associated with sequence quality. However, when I take the ASV sequence and try using blast (NCBI nr) I am able to pickup the genus level taxonomy correctly.
What I want to know is, if there is any other way to improve the taxonomic assignment, to get a genus level assignment (even with little low confidence) for most of my ASVs ??
I tried using vsearch separately for the such ASVs with 0.8 cutoff, and the results are not very convincing.
Thank you for your support!!!