• Sequencing is a tool used by many biology and computing fields to investigate genomes (typically human)
• A DNA sample is processed such that a forward and reverse strand are isolated and indexed
• Using computing you can manipulate this data to do any number of things

• Any type of cell can be used
• The cell and nucleus are broken apart to expose intracellular DNA
• It is then extracted and purified to further isolate the DNA

• DNA is fragmented into smaller chunks, which are cheaper and more flexible to sequence
• Known adapter sequences are added to allow the chunks to be used
• These chunks of DNA are then processed through sequencing machines which “read” the DNA

• Strands of DNA with adapters are put into machines which can index runs of nucleic acid
• A read is known as the smaller fragments of DNA that are sequenced
• A read has a length and orientation associated with it

• Some sequencing technologies have the same read length, no matter fragment lengths
• This means portions of DNA will be read multiple times
• Depth coverage or read depth is the average amount of times that fragments are read over
• The depth can be found with the following formula

Where

• C = Coverage
• N = Number of reads
• L = Read length
• G = Target genome size

\[ C = N * L / G \]

• Always round down, as you cannot physically create extra reads

• Because not all DNA is the same, and sequencing technologies are not perfect, some sections of the DNA will not get sequenced
• The Lander/Waterman model is a good estimation of the probability of bases not getting sequenced based on genome size

Where C = Coverage

\[ P = e ^{(-C)} \]

fig <- plot_ly(data = coverage, x = myX, y = myY, 
               mode = 'lines', height = 325) %>%
layout(paper_bgcolor='#EDEDED', plot_bgcolor='#EDEDED')
fig

• The higher the coverage, the less likely it is that a nucleic acid gets skipped over

Sequencing has many uses including:

• Associating genes with diseases
• Diagnosing disorder and diseases
• Identifying drug targets
• Identifying microorganisms
• Studying gene expression
• Forensic use-cases