we have done quite a bit of work on extending MEGAN to allow processing of Nanopore metagenomic reads (see
https://www.biorxiv.org/content/early/2019/01/04/511683), but we have not yet looked into analyzing Nanopore 16S reads in MEGAN.
This would be my first line of attack: use an alignment tool such as MALT (
http://ab.inf.uni-tuebingen.de/data/software/malt/download/welcome.html) or minimap (
https://github.com/lh3/minimap2) to align against either the Silva database (
https://www.arb-silva.de/download/) or the NCBI 16S database (
ftp://ftp.ncbi.nlm.nih.gov/), then import into MEGAN using a top percent of 5, weighted LCA and Use 16S Percent identity Filter.
If you align against the Silva references, then you should the following mapping file:
If you align against the NCBI 16S references, then use this:
If you do try this and run into any problems/questions, then please let me know