Sean’s Notebook: Olympia Oyster genome…

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.

Data: here

Gap filled Assembly:

Now on to Redundans.

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