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lh3 / minigraph

Sequence-to-graph mapper and graph generator
https://lh3.github.io/minigraph
MIT License
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Translocation not found by minigraph #68

Closed VLoegler closed 2 years ago

VLoegler commented 2 years ago

I am constructing a graph pan genome using several genome assemblies with Minigraph. One of my assembly contain a huge reciprocal translocation between 2 chromosomes: several hundreds of kb at the extremity of the 2 chromosomes are swapped.

However, this translocation seems not to appear when visualising the graph with Bandage. The 2 chromosomes are not linked together.

Is it expected ? Is there an option I could add to allow these kind of links ?

Thanks a lot

lh3 commented 2 years ago

minigraph doesn't support translocations