Linux for large scale sequencing?

Thomas Sicheritz Thomas.Sicheritz at
Wed Feb 11 17:08:58 EST 1998

Arne Elofsson <arne at> writes:

> --Multipart_Fri_Feb__6_11:34:03_1998-1
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> Eugen Buehler <buehler at> writes:
> > 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
> > 
> This differnce is too big. OK solaris is slower than linux but the
> ultraII should be about  the same speed as a pentium II
> > Both were compiled using gcc, optimized.  
> You probably gain a factor of 2 or more using cc (-alotofflags) on
> solarisand about 30 % using pgcc on linux.
> > 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.
> No problems, however NFS prestanda of linux is really bad (sometimes a
> factor of 4 slower than on solaris). So write to local disks when you
> write a lot of data

The NFS is a bit slower in the 2.0.x kernels but is completely rewritten in 
the 2.1.x versions, - but investing in a fast ethercard instead of these
cheap ones people usually put in PC's should give you a 'normal' performance.


Sicheritz Ponten Thomas E.  Department of Molecular Biology
Biomedical Center           Uppsala University
BMC:  +46 18 4714214        BOX 590 S-751 24 UPPSALA Sweden
Fax   +46 18  557723
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