Class 02: Whole genome sequencing. The seminal papers ``Is Whole Genome Sequencing Feasible?'' ``Whole-Genome DNA

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Text of Class 02: Whole genome sequencing. The seminal papers ``Is Whole Genome Sequencing Feasible?''...

  • Slide 1
  • Class 02: Whole genome sequencing
  • Slide 2
  • The seminal papers www.cs.arizona.edu/people/gene/#papers ``Is Whole Genome Sequencing Feasible?'' ``Whole-Genome DNA Sequencing'' ``A Whole-Genome Assembly of Drosophila''``A Whole-Genome Assembly of Drosophila''
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  • Shotgun sequencing Multiply target sequence Break sequences into random fragments Sort by size, discard big and small pieces Insert into bacterial virus (vector) Infect bacterial, and let it reproduce, cloning the insert Read the insert
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  • Definitions G length of target sequence L avg length of read R number of sequencing reads N base pairs sequences = RL I avg length of clone inset c N/G = avg sequence coverage m RI/2G, avg clone or map coverage
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  • Problems Incomplete coverage Sequencing errors (