I have a reference genome that consists only of scaffolds without the assignment of scaffolds to any chromosome. My reference genome is in fasta format.
I would like to extract those sequences that possibly belong to chromosome number 5 of my species. For that, I have a transcriptome de novo assembly from which I have obtained a list of fasta sequences that belong to chromosome 5.
What I would like to do now is to align my fasta sequences beloning to chromosome 5 obtained from transcriptome assembly against the reference genome scaffolds to obtain those scaffolds that belong to chromosome number 5.
My question is that what the best software is for this purpose?
Thank you very much for your help in n advance.