Sean’s Notebook: Olympia Oyster genome assembly in Platanus.
I’ve been trying to incorporate the new PacBio data we recently got and we’ve settled on a combination Platanus/Redundans approach for assembling a new genome from scratch.
I’ve finished the first portion surprisingly quickly. Hooray for Hyak I guess?
Some stats on the final gap closed Platanus assembly:
stats for /Users/Sean/Documents/RobertsLab/Oly__gapClosed.fa sum = 4121175, n = 28721, ave = 143.49, largest = 1971 N50 = 133, n = 10380 N60 = 122, n = 13618 N70 = 114, n = 17127 N80 = 109, n = 20829 N90 = 105, n = 24686 N100 = 100, n = 28721 N_count = 32133 Gaps = 975
Still a lot of gaps. Hopefully the Redundans run with the PacBio stuff will help with that.
Now on to Redundans.