Data integration in microbial genomics ... - Jacobs University

12 1. Introduction
what kind and what they are doing?” To address these questions, it
helps to understand the most important working steps that lead to the
generation of sequence data. Figure 1.7 shows a generalized workflow
in microbial genomics.
Figure 1.7: A generalized workflow for microbial genomics
When it is aimed to analyze genomes from microorganisms, first, biological
samples have to be taken in the field (figure 1.7, step 1). Different
isolation strategies are applied depending on the target organism
(figure 1.7, step 2). Once in pure culture, DNA is extracted (figure 1.7,
step 3) and sequenced (figure 1.7, step 4). Today, complete genomes
are often sequenced, assembled and finally analysed (figure 1.7, step
5). The workflow begins very practically in the field, continues with
technical work in the laboratory and ends with sequence data analysis
on the computer. In metagenomics, DNA is extracted directly from
environmental samples, without applying cultivation techniques, and
either specific genes are amplified and sequenced or random sequencing
is performed. As soon as sequence data is available, it can be
submitted to the INSDC.