[mira_talk] Re: How do you call your ABI traces?

  • From: John Nash <john.he.nash@xxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Fri, 16 Sep 2011 17:43:13 -0400

On 2011-09-16, at 5:34 PM, Bastien Chevreux wrote:

> On Friday 16 September 2011 23:23:36 John Nash wrote:
> > [...]
> > Who do you trust?
> 
> You should forget about the native pregap basecaller. Many sequencing centers 
> I know used phred as part of the pregap package (there either was an import 
> module or they wrote one, I do not recall).
> 
> In the company I previously worked for we had a licence for TraceTuner and it 
> actually did a slightly better job compared to phred, but that is 10 years 
> ago.
> 
> Note: the qualities for the sequences you posted look funny for the 
> TraceTuner called sequence ... they are in the low 0 to 10s and rarely above, 
> while phred is in the 30s for large parts, which is more what I'd expect. You 
> might want to check the options with which you called TT.

Thanks Bastien.  

I used the defaults for ttuner via command line. The java package crashes on my 
Mac and Ubuntu boxes (no Windows here), so I used the command line version 
where the quality options are sparse. I think I'll stick with phred as I am 
used to it.

Have a good weekend. 

John

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