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

Phillip San Miguel via autoseq%40net.bio.net (by pmiguel from purdue.edu)
Wed Feb 25 07:37:05 EST 2009

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.

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