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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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Can cactus account for interchromosomal translocations? #1011

Open andyjslee opened 1 year ago

andyjslee commented 1 year ago

I was wondering if interchromosomal translocations can be included in the graph genome generated by cactus. Thank you for your response!

glennhickey commented 1 year ago

You get them with progressive cactus, but they are excluded by default for pangenomes.

I haven't had a chance to test this at all, so wouldn't recommend it at this point, but you can try to include inter-chromosomal events in your pangenome graph by running the lower level commands (ie as described here : https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md#yeast-getting-started) and not running cactus-graphmap-split.