Software choice? sequencher, phrap/phred/consed, staden?

Bruce Roe BROE at aardvark.ucs.uoknor.edu
Wed Aug 14 08:45:25 EST 1996


Don writes: 
=> Do you have opinions to share on the best choice(s) of 
=> software for small-scale autosequencing?  We have recently acquired
=> Sequencher, Phrap/Phred/Consed/etal, and Staden package,
=> all of which can handle ABI and SCF trace data, do base calling
=> and assembly.  But it will take some time to compare and evaluate
=> these, so your experiences would be valuable to us and others
=> starting with such software.
=> 
=> Thanks,  Don
=> 
=> --
=> -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu
=> 

Don,
        It depends on the platform as Sequencher is on the Mac and many
folks really like it.  Both for performance and because it's Mac-based.
Phrap/Phred/Consed/etal, and Staden package are all unix based and to
many users, that's a big pain as they don't have readily available unix
boxes.  Sure you can use Mac-X and connect but that too is a pain.
        For small-scale projects I'd strongly recommend Sequencher as
it has many advantages to the end user and because it's commercial, is
supported very very well.  For large projects, go with the unix programs,
however, Consed doesn't have some of the features that we find useful
in XGAP/gap4 for editing contigs.  Both also have GREAT difficulty in dealing
with repeat sequences (especially in cosmids, bacs, pacs, fosmids with 40-
300kb inserts).  The jury is still out on which handles these repeats better
Phred/Phrap or Staden, as Phred/phrap has a tendency to make "false" joins
while Staden's xgap/gap4 refuses to make any false joins so a person has to
use "find internal joins" and then (sometimes or most of the time depending
on experience) makes some bad joins anyway.
        None of these programs is ideal, especially with large projects.
But for the small ones's (2-10kb), I'd go with "simplest is best" and stick
with Sequencher.  I know it costs the most, BUT you get what you pay for
and have someone to gripe at that HAS to be responsive or else they loose
business.
        Cheers.......bruce
***************************************************************************
Bruce A. Roe, Ph.D    Department of Chemistry and Biochemistry
                      University of Oklahoma, Norman, OK 73019-0370, U.S.A.
Phone: (405) 325-4912 or 7610; FAX: (405) 325-7762; e-mail: broe at uoknor.edu
********************** http://dna1.chem.uoknor.edu/ *********************** 




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