I like to use blast for taxonomy, however, I want to change naive LCA algorithm to LCA weight (like Megan 6), does anyone have any code or share any idea about wLCA? Can you help me? Thank you.
Hi @Phuc_Hu_nh_Van,
It looks like the weighted LCA in Megan 6 is really specific to Megan 6 (so if you plan to use this, you should just use Megan 6 and you can import taxonomy classifications into QIIME 2 following the importing tutorials). Moreover, this method is really meant for shotgun metagenomics, as the weights are basically a way to guide classification to references that receive an overwhelming number of overlapping hits.
This seems less relevant for marker gene classification, since the sequences (OTUs/ASVs) are all unique sequence variants of the same exact gene and may in fact map to different taxa, not partially overlapping sequences and you are looking for the intersection of hits to a reference sequence. So if you are using 16S or another marker gene, naive LCA is likely more suitable.