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In this chapter, we will cover some of the core aspects of bioinformatics work. We will deeply explore how to examine the quality of sequencing data for different technologies. We will also go deeper into various tools for manipulating relevant file formats and briefly cover some recent advances in data compression for bioinformatics files. Then, we’ll discuss how sequencing data is aligned to reference sequences and review the importance of different aspects of sequencing algorithms. Finally, we’ll get into variant calling and see how the information resulting from an alignment can be used to find critical biological insights about people and organisms.In this chapter, we’re going to cover the following main topics:
- Quality control for sequencing data
- Tools for sequence manipulation
- Sequence alignment with BWA
- Variant calling with FreeBayes
