Does input.fa need to be masked by repeatmasker?

ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs

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Does input.fa need to be masked by repeatmasker? #1533

Closed GooLey1025 closed 2 days ago

GooLey1025 commented 3 days ago

Much thanks for the developer's support! I know minigraph-cacuts pipeline ignore softmask. But I want to make sure whether input.fa need to be masked by RepeatMasker. Perhaps it will increase speed and accuracy. Can you give some suggestions.

glennhickey commented 2 days ago

Please see here:

https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md#frequently-asked-questions