Autosome/ sex chromosome assembly error

Question

[Megan]

Hi,

I'm doing a coverage analysis to identify the W chromosome in a chromosome level genome assembly from a female snake, (the genome on NCBI does not have chromosome names assigned to scaffolds). I found that there was an assembly error in the reference genome, and a chunk of an autosome scaffold is attached to the W scaffold. My question is, what tools can I use to separate out the W from this scaffold and create a new scaffold with just the W? Thanks!