Assembly

Oracle, C/C++; DEC Alpha, Linux compute farms

• Consider pair-wise comparison of 14,000,000 sequences !
• A prime example of coarse-grained parallelism
• Use Oracle DB to create task lists & supervise pull-compute servers
• Complexity is also in setting up and characterizing the suite of heterogeneous compute servers (Alpha 4100, DS-10, 20, various other flavor alphas; linux boxes of various sizes; Solaris)
• Once binned, assemble each bin using PD s/w, to arrive at
  • consensus sequence & qual scores
  • alignment of each input seq to the consensus
  • splice variants

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