TIGR assembler vs PHRED/PHRAP

awalsh at em.agr.ca awalsh at em.agr.ca
Thu Mar 29 04:57:34 EST 2001


For ESTs, I think you might want to try CAP3.  That is what TIGR uses to
create their 
gene indices.  There is a good paper that compares different assembly
programs
for how they handle ESTs (Nucleic Acids Research Vol 28: 3657-3665).

I've used all three and I've found CAP3 most useful, although I haven't really
experimented
much with the other two.  You can view your assemblies with Consed (part of
Phrap package)
if you use the -nophd switch when you call the program.

Hope that helps.

Andrew

In article <5.0.2.1.0.20010228110202.009f8e50 at agri.huji.ac.il>, Na'ama
<shaham at agri.huji.ac.il> writes:
>We'd like to assemble about 1500 rose ESTs, and we are looking for software.
>
>Can you tell me what are the differences between TIGR assembler and PHRAP?
>Which of these programs is more reliable?
>
>Any advise will be appreciated!
>
>
>
>
>
>---
>


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