Thanks buchnfink. Assuming you are the author of diamond, let me ask you a few questions- I used Last to align assembled reads with uniprot database. I then used 'sort-maf-last' script and then blast2rma script to get rma6 file (size=470mb). When I view that output rma6 on Megan, it only shows two nodes. What could be reason for that? So, does DIAMOND also support long read alignment? Based on this web https://ab.inf.uni-tuebingen.de/software/downloads/megan-lr, I thought I can not use DIAMOND for LR.
Long read alignment for MEGAN6
1 answer
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.
Regarding your first question, I can't help you with that, please ask at the MEGAN community website (http://megan.informatik.uni-tuebingen.de/).
DIAMOND does support long read alignment now, it has recently been implemented.
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