Large phrap assemblies

Osborne, Brian brian.osborne at cadus.com
Thu Feb 17 10:18:28 EST 2000


It's been a while since I used phrap on large projects like yours but I'd
have to say your result surprises me. I remember we used an Ultra1 with 256
MB at first, then added more for 512, but even with the largest assemblies
phrap would never run out of memory, it would just go into its heavy swap
mode and slow down, but never actually stop. Do you have enough disk space
for a good swapfile? Has someone limited the size of your swapfile?

Brian Osborne
OSI Pharmaceuticals
777 Old Saw Mill River Rd.
Tarrytown NY USA
brian.osborne at cadus.com
TEL 914 467 6291
FAX 914 345 3565

-----Original Message-----
From: Paul Shinn [mailto:pshinn at mail2.sas.upenn.edu]
Sent: Thursday, February 17, 2000 12:01 AM
To: autoseq at net.bio.net
Subject: Large phrap assemblies

    I can't seem to find the proper forum for this question so I'll ask
If you have someone in your lab who can answer the question, please pass 
it on.
    We have 100-120kb sequencing projects that can exceed 5000 
sequences.  When this happens, phrap runs out of memory and we end up 
finding alternative, more tedious ways to assemble the data.  Our fastest 
machine a Sparc Ultra10, 450Mhz with 384MB RAM doesn't even cut the 
mustard.  There is a departmental machine with 1Gig of RAM that can't 
even do it sometimes.  My question is, what systems are your groups using 
to assemble with phrap?  I think really fast Sparcs get prohibitively 
expensive but it doesn't seem like too many people run Solaris on PCs.  I 
would like to buy a dual processor computer or even a REALLY fast single 
processor model with RAM maxed out to handle this task.  That is unless, 
of course, you have an alternative to this brute force method.


Paul Shinn    
Sequencing Coordinator                                    ,___o
pshinn at neomorph.bio.upenn.edu                            _-\_<,
Arabidopsis thaliana Genome Center                      (*)/'(*)
(215) 573-7256


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