2.1 DNA sequencing data

These days, the vast majority of genomic data is generated through high-throughput Illumina short-read sequencing. The broad steps of this sequencing process are:

  • Extract DNA
  • Fragment DNA
  • Prepare for sequencer (add adapters, etc.)
  • Amplify DNA
  • Sequencing (add fluorescently labeled nucleotides that are read by a digital camera)



Fig. 1 (source). Schematic of Illumina short-read sequencing.
Fig. 1 (source). Schematic of Illumina short-read sequencing.



This sequencing approach is fast and cost efficient, but introduces two main limitations.

  1. Because of the fragmentation step, the resulting sequencing reads are extremely short (~150 bp).
  2. We don’t know where in the genome the sequencing reads came from. (This is a limitation common to nearly every sequencing experiment.)



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