I was working on a pipeline for genome assembly and I have used the human paired-end NGS data.
I want to compare my denovo assembly to the available human genome which is based on Sanger sequencing mainly. How can I compare my denovo assembly to the sanger sequencing inorder to check -
How much of the genome was covered in the denovo assembly?
How many regions of the genome have I missed in the denovo contigs?
Do I compare the contigs or scaffolds to the reference which is ordered as chromosomes?
I know Quast is used to test different genome assembly qualities, but what about comparing a denovo assembly to a reference genome???
I'm afraid Quast is not favorable for bigger genomes. Good for bacterial I guess.