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US Grant. Finally $$$$!!!! Jim Giovannoni (PI), Stephen Stack, Joyce van Eck, Lukas Mueller, Bruce Roe Components: WGS 10x 454 titanium BAC by BAC for chromosome 1 & 10 Physical map Fosmid ends. Physical Map. Repeat physical map with capillary technology

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us grant
US Grant
  • Finally $$$$!!!!
  • Jim Giovannoni (PI), Stephen Stack, Joyce van Eck, Lukas Mueller, Bruce Roe
  • Components:
    • WGS 10x 454 titanium
    • BAC by BAC for chromosome 1 & 10
    • Physical map
    • Fosmid ends
physical map
Physical Map
  • Repeat physical map with capillary technology
  • 53,000 of the target 100,000 BACs done
  • The revised estimate is completion of fingerprinting by mid-August and draft physical map apx. September 1.
  • HindIII - 26,880 - 70 plates (completed)
  • EcoRI - 26,880 - 70 plates (completed)
  • Mbo1 - 23,040 - 60 plates (starting next week)
  • Sheared - 23,040 - 60 plates (starting apx. early August )
  • 140 of 260 plates completed.
whole genome shotgun
Whole Genome Shotgun
  • 2 runs on 454 titanium
  • WGS ~3Kb average fragment size
  • WGS paired-end libraries from fragments averaging ~3Kb and ~8Kb (what they want to call a 3Kb and 8Kb "jump")
  • the equivalent of half a billion bases (half of which are 3Kb paired ends)
  • Reads too short (~220bp/read)
  • Working on it!!!!
genome assembly
Genome assembly
  • Hardware
    • 128GB RAM 16-processor core system available at SGN
  • Software
    • Mira, cabog, newbler