I have a dataset obtained with Illumina Miseq with 2*250 sequencing reads on the full lenght fungal ITS region. As the amplicon is longer than 600 bp, my R1 and R2 reads do not overlap. My objective is to obtain OTU/ASV table with taxonomic classification
I have already performed "classical" picking and taxonomy assignment (USEARCH) independentrly for the R1 and R2 reads, with overall comparable results. The taxonomy classification, however, is not particularly good as lots of OTUs got classified in SH at the sp. level.
I would like to improve taxonomic classification (if possible) over using only the R1, and I was looking around for methods for mapping non-overlapping reads on the UNITE database retaining taxonomic information (as for now, candidates could be CENTRIFUGE or KRAKEN as far as I understood).
I was wondering, before really beginning to test, if this approach would actually give me better taxonomic classification results or if I would end up with results very similar to what already obtained for the R1 alone.
Does anyone have experience with something similar? Did anyone obtain better taxonomic classification (i.e. higher number of species level identification) with read alignment respect to R1 alone?