The question of how long does it take to assemble X specie comes up often.
I thought I would share my experience and some results.
A ~2.7G genome.
4 different librairies of the same individual
1 lane of hiseq each (lots of molecule diversity)
I have mates but didn't put them in, will scaffold with something else.
Although I will rerun with the mates to see how Ray fairs latter.
2025 cores (distributed mpi), on 85 nodes
cput=1044:55:24,walltime=43:53:52
Ray settings:
-read-write-checkpoints ${RAY_WORK_DIR}/checkpoints \
-show-memory-usage \
-route-messages \
-connection-type polytope \
-routing-graph-degree 88 \
Output :
Contigs >= 100 nt
Number: 3287924
Total length: 2959541162
Average: 900
N50: 8158
Median: 119
Largest: 175227
Contigs >= 500 nt
Number: 588712
Total length: 2588045901
Average: 4396
N50: 9851
Median: 1860
Largest: 175227
Scaffolds >= 100 nt
Number: 3256053
Total length: 2964597718
Average: 910
N50: 8758
Median: 119
Largest: 175227
Scaffolds >= 500 nt
Number: 559885
Total length: 2594461126
Average: 4633
N50: 10569
Median: 1931
Largest: 175227
I'm very happy with the result!
Louis
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