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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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Working on highly-fragmented draft assemblies #1025

Closed xiaoyezao closed 1 year ago

xiaoyezao commented 1 year ago

Hi Cactus designer,

I am working on a plant genera (13 species) with one reference-level assembly and 12 fragmented draft assemblies (100k-200k scaffolds) and the genomes are highly repetitive (~65%). Do you have any suggestions on genome alignment using Cactus?

Thank you,

Xiaoyezao

glennhickey commented 1 year ago

Make sure they are well softmasked with RepeatMasker and/or RepeatModeller.