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Development of Efficient Algorithms and Technologies for Structural Variation Detection by Single Molecule Sequencing

SOF107
  • Project Leaders: Cenk Sahinalp, Inanc Birol
  • Institutions: Simon Fraser University (SFU)
  • Budget: $68,000
  • Competition: Science Opportunities Fund - Round 1
  • Genome Centre(s): Genome BC
  • Fiscal Year: 2009
  • Status: Closed

The goal of this project was to develop a novel and efficient algorithms for managing, filtering and analyzing data generated by these platforms, both for main stream PCs as well as newly emerging architectures that enable simple and effective parallelization of these algorithms. The progress towards achieving strategic outcomes is excellent. First results using MrFAST were published in Nature Genetics (highest impact factor in the field of Genetics) and the vastly expanded version of MrFAST (MrsFAST) appears to be even more accurate and much faster. Both mapping algorithms have been verified on reads produced by various technologies and the results are exceptional. In summary, the project has produced industrial quality source code for mapping and made it available through Sourceforge.  Both GSC and NCBI are currently using these versions. The project has been very successful with future collaborations and many local and international researchers have contacted the project leaders to collaborate on Structural Variation studies among individual genomes.