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.
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.
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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