Chapter 1, Python and the Surrounding Software Ecology, tells you how to set up a modern bioinformatics environment with Python. This chapter discusses how to deploy software using Docker, interface with R, and interact with the IPython Notebook.
Chapter 2, Next-Generation Sequencing, provides concrete solutions to deal with next-generation sequencing data. This chapter teaches you how to deal with large FASTQ, BAM, and VCF files. It also discusses data filtering.
Chapter 3, Working with Genomes, not only deals with high-quality references—such as the human genome—but also discusses how to analyze other low-quality references typical in nonmodel species. It introduces GFF processing, teaches you to analyze genomic ...
