Sean’s Notebook: Canu run finished

Looks like Hyak finished it’s Canu assembly for the Oly PacBio data over the weekend, and here are the statistics for it.

[seanb80@mox2 oly-test]$ /gscratch/srlab/programs/canu/Linux-amd64/bin/tgStoreDump -sizes -s 50000000 -T /gscratch/srlab/data/CanuTest/oly-test/unitigging/oly_pacbio_.ctgStore 2 -G /gscratch/srlab/data/CanuTest/oly-test/unitigging/oly_pacbio_.gkpStore
lenContig ng10       23155 bp   lg10     175   sum    5001399 bp
lenContig ng20       19201 bp   lg20     416   sum   10012857 bp
lenContig ng30       16610 bp   lg30     697   sum   15014659 bp
lenContig ng40       15073 bp   lg40    1014   sum   20013348 bp
lenContig ng50       13606 bp   lg50    1364   sum   25008188 bp
lenContig ng60       12421 bp   lg60    1749   sum   30009994 bp
lenContig ng70       11361 bp   lg70    2170   sum   35007399 bp
lenContig ng80       10115 bp   lg80    2634   sum   40002506 bp
lenContig ng90        8041 bp   lg90    3178   sum   45002283 bp
lenContig sum   46288879 (genomeSize 50000000)
lenContig num       3388
lenContig ave      13662

13.6 kbp NG50 is an improvement! Next, polishing with Pilon.