Is there any application can convert gff3 file and related fasta files into ace file or sam file? I dont want to reinvent the wheel.
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I don't understand what you want to do - going from GFF3 to ACE or SAM makes no sense.
You store annotation in GFF3 files (e.g. there is a gene at this location), but neither ACE nor SAM hold that kind of annotation (they are assembly/mapping files, e.g. this read mapped to this contig at this location).
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