The Problem

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The Problem

• In standard production, the contigous length of a
  sequence read is about 400 800 bases.

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The Problem

• In standard production, the contigous length of a
  sequence read is about 400 800 bases.

Working draft of the Human Genome 3 000 000 000
base pairs Nature (2/15/01) , Science (2/16/01)
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Shotgun Sequencing
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Shotgun Sequencing
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Problems in Shotgun Sequencing

• Repeated regions
• Base-calling errors
• Unknown orientation
• Incomplete coverage
• Contamination
• Unremoved vector sequences
• Polymorphisms

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Repeats
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Repeats
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Base Calling ErrorsBase Quality
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Mate Pairs
1000 bp
500
Read.s
Clone insert
Read.r
500
2000 bp
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Mate Pairs
R1
R2
R3
R4
R5
R6
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Ref
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System 20 - 454 Life Sciences
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Solexa
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The read length

• 454
• 200 bases.
• Capillary sequencers, Sanger method
• 800 bases.
• Solexa
• 25 bases.