Linux for large scale sequencing?

Eugen Buehler buehler at cbil.humgen.upenn.edu
Wed Jan 28 17:45:46 EST 1998

I would like to hear from anyone that is using Linux in
a large scale sequencing project, particularly for programs like
phred, phrap, the Staden package, acedb, blast, etc.  I compiled
phrap on my new Dell at home and compared the time it took to
assemble a relatively large (2700 sequences) project.  The results:

Dell XPS Pentium II 300MHz, 64MB RAM, RH Linux 5.0:      11 minutes
Sun Ultra2 Creator 3D, 300MHz, 128MB RAM, Solaris 2.5:   40 minutes

Both were compiled using gcc, optimized.  Considering the
difference in price between these two machines, I'ld like to
consider using PC's running Linux if we buy more workstations.
Also of interest would be experiences people have networking
between Solaris and Linux through NFS filesystems.

Eugen Buehler
Arabidopsis thaliana Genome Center
University of Pennsylvania
buehler at cbil.humgen.upenn.edu

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