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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. Repeat physical map with capillary technology

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US Grant

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  1. 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

  2. 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.

  3. 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!!!!

  4. Genome assembly • Hardware • 128GB RAM 16-processor core system available at SGN • Software • Mira, cabog, newbler

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