Advanced NGS Data Processing
If you work with next-generation sequencing (NGS) data, you know that quality analysis and processing are two of the great time-sinks in getting results. In the first part of this chapter, we will delve deeper into NGS analysis by using a dataset that includes information about relatives – in our case, a mother, a father, and around 20 offspring. This is a common technique for performing quality analysis, as pedigree information will allow us to make inferences on the number of errors that our filtering rules might produce. We will also take the opportunity to use the same dataset to find genomic features based on existing annotations.
The last recipe of this chapter will delve into another advanced topic using NGS data: metagenomics. We will QIIME2, a Python package for metagenomics, to analyze data.
If you are using Docker, please use the tiagoantao/bioinformatics_base image. The QIIME2 content has a special setup process that will be discussed...
