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SUMMARY:Next generation computing for next generation sequencing - Arndt v
 on Haeseler (Center for Integrative Bioinformatics Vienna)
DTSTART:20100215T160000Z
DTEND:20100215T170000Z
UID:TALK21652@talks.cam.ac.uk
CONTACT:Florian Markowetz
DESCRIPTION:High throughput sequencing provides access to important inform
 ation on genes\, their function and genetic variation on genomes. One way 
 of post processing is a reference guided assembly. For this approach\, one
  needs an evolutionary closely related reference genome. However\, in the 
 end of 2009\, only a few completely referenced organisms are available. Th
 erefore\, we have also considered more distantly related organisms as refe
 rence candidates. In this study\, we investigate the usability of the grap
 hics card to gain speed and accuracy in mapping the reads. Further\, we co
 mpare the performance of different assembly programs taking false positive
 s into account. Here\, we defined a false positive rate based on the numbe
 r of misplaced or missing nucleotides per mapped read. This not only gives
  an indication of the possible missing SNPs\, but it also takes the edge e
 ffect of local alignment into account. We show that our approach is more a
 ccurate compared to currently used\, and it achieves performance improveme
 nts of up to 112 fold\, by using the graphics card.\n\nJoint work:\nFritz 
 Sedlazeck 1\;2\;3\;4\, Greg Ewing 2\;5 & Arndt von Haeseler1\;2\;3\;4\n\n1
  Center for Integrative Bioinformatics Vienna (CIBIV)\, Max F. Perutz Labo
 ratories\, Vienna\, Austria\n2 University of Vienna\, Vienna\, Austria\n3 
 Medical University of Vienna\, Vienna\, Austria\n4 University of Veterinar
 y Medicine\, Vienna\, Austria\n5 Mathematics and BioSciences Group (MABS)\
 , Vienna\, Austria
LOCATION:Cancer Research UK Cambridge Research Institute\, Lecture Theatre
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