[Automated-sequencing] phrap contig ,apply contig quality values?

Umanga via autoseq%40net.bio.net (by aumanga from biggjapan.com)
Wed Feb 25 01:45:51 EST 2009


Greetings all,
Firstof all, come from Computer science background ,so I have very little
knowledge in Bioinformatics.
Now  my question ;
I assemble AB1 files using phred/phrap.I noticed that after assembling using
'phrap', it generates contig file (say 'seq.contigs') and a contig-quality
file ('seq.contigs.qual').

Now,I want to get the same contig which generated by ChromasPro using phrap.

I noticed that ,if I ignore the config bases with quality value '0' (which
stored in seq.contigs.qual) , I can get almost same sequence as ChromasPro.
Is this correct?
This there a parameter to do this in 'phrap' itself? 

Thanks in advance,
Umanga
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