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I've got an annotated draft genome assembly made using short and long read strategies. I've also done optical mapping to stitch some of the contigs together, with the goal being chromsome-length assemblies. How do I annotate the output .fasta from the optical mapping assembly using the .gff of the draft assembly that was used as input? I also have a .agp file that describes what sequence fragments ended up where in the output.

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You should use a liftover approach. You could either do this based on exact changes, which might be a bit tedious given the presumably large number of join operations you've done (especially if you've e.g. broken contigs).

Therefore it might be more convenient to do it on the basis of homology.

liftoff is one simple tool for doing this with a gff file and your 2 fasta files. It seems to mostly work ok.

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