phrap quality scores

Rachel M. Kadel-Garcia rgarcia at is06.fas.harvard.edu
Sat Jan 8 00:14:54 EST 2000

In article <387698C5.EEA17FB at cellworks.mbt.washington.edu>, 
Stephen R. Lasky wrote:
>"Rachel M. Kadel-Garcia" wrote:
>> Does anyone here have an understanding of phrap quality scores
>> beyond what's in the docs?  I'm trying to figure out how to
>> assign similar quality scores to assemblies not done with phrap,
>> and I'm resorting to spelunking in the source, but it's rough
>> going.
>>                                                 Rachel
>Phrap, I believe, is not the program assigning the quality scores. 
>Phred is.  Phrap uses the phred quality scores to do its alignments.

Phred assigns quality scores to bases in individual reads.  Phrap uses
those quality scores and various things about the alignments to generate
consensus quality scores.

>Do you have the Phred docs? 
>I presume that you don't have the chromats, otherwise you could run them
>through phred and get the quality scores.

I have the phred docs and the chromat files, but that won't get me
consensus quality scores.


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