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

Stefan Weckx sweckx at uia.ua.ac.be
Thu Jan 27 07:38:20 EST 2000

Finally an interesting talk now in this newsgroup! At our lab, we are in
a setup phase playing a little bit around with Staden and the Washington
packages. Concerning Gap4 vs. Consed, I'm a little biased since we
worked more with Gap4. 
I have actually a problem by integrating phred in Pregap4:

- Phred -
Thu 27 Jan 13:31:20 2000 phred: phred produced unknown filename:
Renamed file  to SCF_fofn.scf_dir/122533a.t3SCF.
can't read "file_id()": no such element in array
    while executing
"set file_id($f) $file_id($f2)"
    (procedure "phred::run" line 60)
    invoked from within
"${mod}::run $files"
    (procedure "run_modules" line 14)
    invoked from within
"run_modules $files"
    invoked from within
"if {!$interactive} {
    if {[check_modules 1] > 0} {
	verror ERR_WARN check_modules \
	    "One or more modules have not been config..."
    (file "/usr/local/staden/linux-bin/pregap4" line 86)

Does someone knows how to solve it?

We tried also the assembler Mira from Bastien Chevreux at DKFZ in
Germany (http://www.dkfz-heidelberg.de/mbp-ased/). It gives also nice
results. Problem is that the output is in CAF format and that one needs
a program caf2gap (Sanger). I had a problem to compile it for Linux. Has
anyone done it so far and succeeded?



Stefan Weckx				
Laboratory of Molecular Genetics - VIB	
Department of Biochemistry			 	
University of Antwerp				 
Universiteitsplein 1				 
B-2610 Antwerpen - Wilrijk

James Bonfield wrote:
> In article <388FBFE5.1065EE90 at mail.ru> Volodya <bo-ba at mail.ru> writes:
> >       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.
> Hello Volodya,
> I implemented the use of phred scores within Gap4 so I can explain how
> this works, although I think that the best source of information for
> Gap4 is in the following web pages:
> http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_121.html#SEC194
> http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_122.html
> http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_55.html#SEC85
> For what it's worth, the Sanger Centre are now routinely using Gap4 in
> the "confidence" consensus mode to direct their final editing. The
> original estimates showed that this final editing stage was sped up
> around 7 fold (compared to their original strategy of checking all
> discrepancies not automatically fixed by auto-edit) with comparable
> final consensus accuracy.
> I cannot well explain how this compares to Consed. I have only seen
> consed once, and I didn't use it myself. Indeed we have deliberately
> avoided asking for a copy of Consed to ensure that our ideas are fresh
> (although sometimes the solution is obvious). However from what I gather
> consed cannot calculate a consensus itself. Rather it uses the
> consensus given to it by phrap. Hence the confidence values assigned
> to consensus bases are those that phrap determines. Unfortunately we
> can no longer obtain any newer versions of phrap, so I do not know how
> well the newest versions compare to the release we have (0.960731),
> but I believe the phrap consensus algorithm has been recently changed.
>         James
> --
> James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 213556
> Medical Research Council - Laboratory of Molecular Biology,
> Hills Road, Cambridge, CB2 2QH, England.
> Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/

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