How to find nonhomologous DNA sequences between 2 speices

[lwgcc]

I want to indentify a non-human species(B ,the genome size is about 100Mb) from the mixture of human and B species by target sequecing method.
so the first thing is to find the nonhomologous DNA sequences between two species(human and B species) from genome.fa file ,and generate the *.fa file which includes the sequeces specifically in B species but no in human.
So can anyone introduce me a software to find nonhomologous DNA sequences between them?
Thanks!

[GenoMax]

I want to indentify a non-human species(B ,the genome size is about 100Mb) from the mixture of human and B species by target sequecing method.
so the first thing is to find the nonhomologous DNA sequences between two species(human and B species) from genome.fa file ,and generate the *.fa file which includes the sequeces specifically in B species but no in human.
So can anyone introduce me a software to find nonhomologous DNA sequences between them?
Thanks!

For this initial analysis have you considered using BLAT? What is the status of genome sequence for species B (contigs, chromosomes)? Is species B related to humans?

BBSplit.sh from BBMap suite would be ideal when you are actually ready to assign NGS sequences to individual genomes.