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

[Umanga]

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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[Phillip San Miguel]

Umanga wrote:
> 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

Hi Umanga,
Yes, you should remove the bases with zero quality values from the ends
of phrap contigs. A quality value of zero indicates the base call is
random noise. I usually trim the ends of contigs back until I hit the
first base with a 20 or higher quality value.
I don't know of a method to force phrap to do this. It would be nice.
I've never used Chromas or ChromasPro. But different assembly engines
may produce different contigs from the same data set.
Phillip