Genomics in the AWS Cloud

CHAPTER 4The Bioinformatics Workflow

This chapter is concerned with the overall workflow of bioinformatics, in which we go from a tissue sample all the way to a meaningful genome as complete as possible, identifying the places where the test subject's genome differs from the rest of the species.

We cover the process of taking some biological material—some cells—and extracting their genetic material. We explain how to convert the extracted genetic material—the DNA, in the case of most cells from complex organisms—and convert that into data that can be manipulated by an electronic computer. Following that, we show an overview of the bioinformatics workflow that will enable us to derive meaningful information from the data.

The process begins in a “wet lab,” with manipulation of actual cells. (We'll focus on human blood.) From there, a sequencing machine will convert the cells to data—an identified sequence of nucleotides, complete with a statement of how likely each nucleotide identification is to be accurate. After that, it's a matter of cleaning up the sequence to remove as many of its flaws as possible, before aligning it to a reference genome. With the alignment complete, it should be possible to see how the person from whom the sample was taken differs from the species average—and that variation is where the value of genomics is.

In this chapter, we will look at the essentials of practical genetics and bioinformatics. We will examine the processes, tools, and forms of data ...