Assemble nuclear genome from total DNA reads
I have a total DNA reads of a cinnamon sample from illumina hiseq sequencing. I need to assemble the nuclear genome from total DNA reads. I am thinking of using the de nova assembly method. But I'm not sure how to extract nuclear reads from total DNA reads. I need help in extracting nuclear DNA from total DNA and assemble the nuclear genome.
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just asking, but if you already have a reference genome why do you want to run a de novo assembly of a plant genome with only illumina hiseq reads? Do you think you will get a better assembly?
Cinnamon genome has not been sequenced so there is no reference available. Closest genome seems to be camphor tree from the same family.
my bad... I googled "cinnamon genome" and instead it was the genome of a cat called Cinnamon...
these might help you: Best way to remove contaminants to get nuclear genome; How can I use BLAST to extract chloroplast sequences from DNA reads?