I think it would be very useful to create an "alignment viewer" that compares an alignment versus a reference which can show insertions /deletions/matches/mismatches
This can be seen as in some ways similar to synteny in some ways, as a genome-to-genome is basically a large scale alignment, but a large scale genome-to-genome will probably be broken up into multiple alignments that get chained together (small scale example of MT-human vs MT-orang in minimap2 docs is a single alignment and can output SAM)
I think it would be very useful to create an "alignment viewer" that compares an alignment versus a reference which can show insertions /deletions/matches/mismatches
This can be seen as in some ways similar to synteny in some ways, as a genome-to-genome is basically a large scale alignment, but a large scale genome-to-genome will probably be broken up into multiple alignments that get chained together (small scale example of MT-human vs MT-orang in minimap2 docs is a single alignment and can output SAM)