I am trying to use MEGAN6. I have assembled transcriptome data that I want to align with nr database. What options do I have for long read alignments (beside LAST) that I can then import to MEGAN6?
You can use DIAMOND (https://github.com/bbuchfink/diamond) for long read alignment. It now also supports frameshift alignments. Use the options -F 15 --range-culling.