Staden (with phred/phrap) vs. Consed (with phred/phrap)

Paul Shinn pshinn at mail1.sas.upenn.edu
Wed Jan 26 21:30:30 EST 2000


Volodya (bo-ba at mail.ru) wrote:
: Hello,

: 	I would appreciate sharing any first-hand experience in using Staden
: and Consed both with phred and phrap. I am interested in knowing any
: issues that may affect the performance and usability (availability of
: latest versions, easynnes of installation, let alown bio-functianality).
: Thanks a lot in advance.

    I have used Gap4 for the past 2 years so I am a little biased.  We 
have a script that tranlates phrap's output into a Gap4 format.  Gap4 can 
integrate phrap but I have yet to see this happen without a lot of 
playing around.  I am still trying to make it work right.  I like the 
Gap4 color scheme.  It's much easier on the eyes.
    Consed walks almost hand in hand with phred and phrap.  It was SO 
EASY to setup.  However, I'm not crazy about the colors and the finishing 
approach is one that I'm not accustomed to.  However, I'm sure it is 
sound and with a little practice I would probably like it, too.  Consed 
can also pick finishing reactions every time it runs and also gives you 
oligos to order.  The output is junky but I'm sure it would be easy to 
reformat with a perl script.
    I would think it would be easier to use consed from the outset, 
though.  You simply e-mail the phrap/phred group for their program and 
then you download consed.  Of course you need permission to do so.  I 
believe Gap4 is also freely available.

						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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