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: [email protected] > > To: [email protected] > > 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]] > > > > > > _______________________________________________ > > > Bioc-sig-sequencing mailing list > > > [email protected] > > > 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 > > > > _______________________________________________ > > Bioc-sig-sequencing mailing list > > [email protected] > > 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 [[alternative HTML version deleted]]
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