how to gain the chain information from two genomes

[zhoudreames]

I want to use my assembled genome to liftover reference genome, how to do it? thanks ~

[milkschen]

LevioSAM2 lifts aligned reads from one reference to another using a chain file. If you have a new assembly, you can generate chain files using the nf-LO pipeline and lift alignments to a target reference of interest.