Question: Long read alignment for MEGAN6
1
gravatar for MAPK
4 months ago by
MAPK1.3k
United States
MAPK1.3k wrote:

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?

ADD COMMENTlink modified 4 months ago by buchfink100 • written 4 months ago by MAPK1.3k
2
gravatar for buchfink
4 months ago by
buchfink100
buchfink100 wrote:

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.

ADD COMMENTlink written 4 months ago by buchfink100

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.

ADD REPLYlink modified 4 months ago • written 4 months ago by MAPK1.3k
1

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.

ADD REPLYlink written 4 months ago by buchfink100
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