Identification of chloroplast genome in whole genome contigs

Question

[faizansaleem1992]

Hello,

I have a whole genome contigs from a certain plant specie and I would like to identify the chloroplast genome in those contigs, can anyone please guide me through the process. I will be very much thankful to you.

Best regards.

[GenoMax]

If the chloroplast genome is available in NCBI then follow the instructions in @Pierre's post here: How can I use BLAST to extract chloroplast sequences from DNA reads?

You could also use bbsplit.sh from BBMap suite to separate the plant genome reads from chloroplast ones.

Answer 1

[bioramg]

Hi, I am using velvet for chloroplast genome assembly. what platform are you using for genome sequencing? If you want to do by denova assembly, then use cutoff more than 500x and please let me know the insert size of your library and all... All the very best.