search

ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
Other
481 stars 106 forks source link

Can Cactus be applied to plant genomes? #1374

Open Galaxy-228 opened 1 month ago

Galaxy-228 commented 1 month ago

Hi, The introduction of the Cactus software mentions "It can be used to align hundreds of vertebrate genomes." So, can it be applied to plant genomes?

Thanks so much.

glennhickey commented 1 month ago

Plants can be very difficult to align, but people have used Cactus for plant genomes before. Ex: https://doi.org/10.1093/plcell/koab026

I'd recommend trying to align a small subset of your genomes of interest to get an idea how it performs for your data.