It may be worth trying miniprot for spliced alignments as an alternative path for generating these exon support results.
Though in my tests I found it didn't always get the full alignment splicing boundaries so may need some additional testing. But this combines the search (diamond/tblastn) + spliced align (exonerate) steps and maybe potentially faster?
It may be worth trying miniprot for spliced alignments as an alternative path for generating these exon support results.
Though in my tests I found it didn't always get the full alignment splicing boundaries so may need some additional testing. But this combines the search (diamond/tblastn) + spliced align (exonerate) steps and maybe potentially faster?