[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.
Phillip
	



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