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.

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

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