Genome comparison

[NGS_New_User]

Hi wise people.
I have assembled two genomes of a non-model organism via de novo assembly, a male and female assembly. I want to compare the male and female genome to check out what differences and/or similarities are present, and or any unique reads.
My question is, what tools/software can I use to achieve this goal (have a comparison)?
I am quite desperate and will appreciate any suggestions, ideas and comments.
Thank you!!

[gsgs]

http://magictour.free.fr/seq/epifox[remove if really trusted].exe

[NGS_New_User]

help...

Hi wise people.
I have assembled two genomes of a non-model organism via de novo assembly, a male and female assembly. I want to compare the male and female genome to check out what differences and/or similarities are present, and or any unique reads.
My question is, what tools/software can I use to achieve this goal (have a comparison)?
I am quite desperate and will appreciate any suggestions, ideas and comments.
Thank you!!

Hi again, I am guessing there might not be a specific bioinformatics tool that can accomplish the goal of comparing two genomes. So, re-phrasing my question, what could be a possible pipeline that could lead to finding differences/similarities between two assembled genomes of different sexes? Thanks