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
------------------------------------------------------------------------------
Don't let slow site performance ruin your business. Deploy New Relic APM
Deploy New Relic app performance management and know exactly
what is happening inside your Ruby, Python, PHP, Java, and .NET app
Try New Relic at no cost today and get our sweet Data Nerd shirt too!
http://p.sf.net/sfu/newrelic-dev2dev
_______________________________________________
Denovoassembler-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
