Chapter 3.1 Three Generations of Sequencing

High Throuhput swquence and read mapping

Outline

• Sequencing technologies
• Fastq and FASTAQC
• Sequence mapping algorithms:
  • seed
  • Siffix Array.
  • Borrows-wheeler transformation & LF mapping
  • BW alignment
• Alignment output: SAM and BED

1st Generation: Sanger Sequencing

• add single-stranded DNA sequence to four test tubes.

• Each tube contains all dNTPs + one ddNTP.

• ddATP

• ddCTP

• ddTTP

• DDGTP

2nd Generation: Illumina Sequencing Cluster Generation

widely popular Massivaly paraller Sequencing

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Third Generation Sequencing

• single molecule Sequencing : use polymerase and/or pores for Sequencing without DNA amplification.

• Fewer but much longer reads: good for long sequences, but not for read count application

• Technology still under active development

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