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

Volodya bo-ba at mail.ru
Wed Jan 26 22:47:49 EST 2000

Hello Paul,

	Thank you very much for your input. What do you think about the use of
phred scores in Staden and Consed? I am interested in using that package
that allows fuller usage of this objective quality measure, and possibly
a lesser human intervention and better integration within the automated
system. Are Consed and Staden equivalent in this regard, if they are set
up to use phred and phrap? On the other note, is it too much to ask you
to send me your perl script? It would be very useful for a quick test
drive of Staden/phred/phrap package, since I hear that setting it might
be a problem.

Best regards,


Paul Shinn wrote:
> 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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