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Gaius-Augustus / Augustus

Genome annotation with AUGUSTUS
http://bioinf.uni-greifswald.de/webaugustus/
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Create hints using ONT data. #386

Closed eprdz closed 1 year ago

eprdz commented 1 year ago

Hi,

I was wondering if it is possible to use ONT data to incorporate hints, and if so, whether I should incorporate this data as PacBio long-read data (so GMAP is used) or as cDNA sequences (and BLAT will be used).

Thanks in advance!

MarioStanke commented 1 year ago

I am not sure. I suppose you can try the GMAP-based approach described here: https://bioinf.uni-greifswald.de/bioinf/wiki/pmwiki.php?n=Augustus.PacBioGMAP The very recently released BRAKER3 follows a transcriptome assembly approach. That may now be a better approach but youprobably have to try it out.

eprdz commented 1 year ago

Great, thank you for your answer.