Large phrap assemblies

Paul Shinn pshinn at mail2.sas.upenn.edu
Thu Feb 17 00:01:21 EST 2000


    I can't seem to find the proper forum for this question so I'll ask here.
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

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






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