I would like to ask about the "diploid" option more. I used 59.5X coverage Illumina reads for polishing 500 Mb plant genome. After polishing, the total length of the assembly increased 9 Mb. Since this diploid plant is selfing-pollinating species, the heterozygosity is low. I want to know whether I should add "diploid" option when I ran with pilon?
Dear community,
I would like to ask about the "diploid" option more. I used 59.5X coverage Illumina reads for polishing 500 Mb plant genome. After polishing, the total length of the assembly increased 9 Mb. Since this diploid plant is selfing-pollinating species, the heterozygosity is low. I want to know whether I should add "diploid" option when I ran with pilon?
The code I used is below:
The summary of the original assembly:
The summary of assembly after polished by Pilon one time:
Thank you!