search

ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
Other
521 stars 111 forks source link

Can I use cactus to compare multiple Poaceae plant genomes? #1487

Open liuyt57 opened 1 month ago

liuyt57 commented 1 month ago

Can I use cactus to compare multiple Poaceae plant genomes? These genomes include diploids, tetraploids, hexaploids, and how does cactus perform in this complex comparison? Is the final calculated phyloP value accurate? Thank you very much!

glennhickey commented 1 month ago

cactus-pangenome should support any ploidy, but is likely not sensitive enough to align different plants.

Progressive Cactus may work better. To align your diploids, tetraploids, etc, you will need to tree them as separate genomes and make a tree out of them.

ex (A_hap1, A_hap2), (B_hap1, B_hap2, B_hap3, B_hap4) etc (except with branch lengths). For anything beyond diploid this will require editing cactus_progressive_config.xml to have allow_multifurcations="1" ( you can also copy the file, edit it, and pass it back in with --configFile).

Some people report that AnchorWave with Cactus improves performance on plant genomes.

liuyt57 commented 1 month ago

Thank you for your reply! I will give it a try.