Hi Dave,

we just started implementing methods for reading the binary .sff files 
and creating a basic quality report similar to the functionalities 
provided by the GS Run Browser. Then, we want to implement Variant 
calling for amplicon projects. That will probably last a few (2-4) months.

Best,
Hans-Ulrich



On 16/02/11 18:31, David A. wrote:
> Hi Hans-Ulrich,
>
> thanks for your prompt answer. Any chance you could give an 
> approximate timeshift for this upgrade? I am very interested in that, 
> I wonder if you could keep me posted. I will also keep an eye on the 
> package webpage for any updates.
>
> Best,
>
> Dave
>
> > Date: Wed, 16 Feb 2011 18:02:18 +0100
> > From: h.klein@uni-muenster.de
> > To: bioc-sig-sequencing@r-project.org
> > Subject: Re: [Bioc-sig-seq] R453Plus1Toolbox
> >
> > Hi Dave,
> >
> > that is right. The manual of Roche's AVA software says: "The automatic
> > Variant detection does not currently report insertions or monomer
> > deletions shorter than 3 bases." At this time, the R453Plus1Toolbox 
> does
> > not implement an indel calling algorithm but relies on the results
> > reported by the AVA software.
> > Since it seems that Roche is not going to solve this issue, we have 
> this
> > topic on our to-do list for our package.
> >
> > Best,
> > Hans-Ulrich
> >
> >
> > On 16/02/11 13:43, David A. wrote:
> > > Hi, I have found a package called R453Plus1Toolbox for analysis of 
> Roche's sequencing data. As far as I know, using AVA, 1bp indels are 
> filtered off fro mthe results to avoid false positives. They can be 
> seen by going to the flowgrams of the region, but they are not part of 
> the output table. Does anyone know if R453Plus1Toolbox can detect them?
> > >
> > > Thanks,
> > >
> > > Dave
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
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> > > Bioc-sig-sequencing@r-project.org
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> > >
> >
> >
> > --
> > Hans-Ulrich Klein
> > Institute of Medical Informatics
> > University of Münster
> > Domagkstraße 9
> > 48149 Münster, Germany
> > Tel.: +49 (0)251 83-58405
> >
> > _______________________________________________
> > Bioc-sig-sequencing mailing list
> > Bioc-sig-sequencing@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing


-- 
Hans-Ulrich Klein
Institute of Medical Informatics
University of Münster
Domagkstraße 9
48149 Münster, Germany
Tel.: +49 (0)251 83-58405


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