SCF format and Staden's 1995 paper

Bastien Chevreux chevreux at mbp-lserv1.inet.dkfz-heidelberg.de
Thu Mar 2 14:44:31 EST 2000


On Wed, 01 Mar 2000 23:25:15 -0500, Volodya <BO-BA at mail.ru> wrote:
>	In the Staden's 1995 paper the SCF file format specification provides
>all four (for A, C, G, and T) not just the highest, quality measures for
>each basecall in a read. What happened with this requirement since 1995?
>Since the present standard quality measure is the phred score, what is a
>way to get four phred scores for each basecall? Phred documentation is
>silent about this. Any pointers would be appreciated. 

A perfect example for a good idea that hasn't been picked up by the
commmunity. Ok, I admit that there are also good arguments against having
these additional quality values, but I think the advantages outweight the
disadvantages.

However, as we did not find any program generating sensible values (or
even generating phred qualities), we discontinued the support in our
shotgun sequence assembler MIRA (http://www.dkfz.de/mbp-ased/). Sad, but
true.

Salut,
       Bastien

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