Bioinformatics with Python Cookbook

Chapter 2. Next-generation Sequencing

In this chapter, we will cover the following recipes:

• Accessing GenBank and moving around NCBI databases
• Performing basic sequence analysis
• Working with modern sequence formats
• Working with alignment data
• Analyzing data in variant call format (VCF)
• Studying genome accessibility and filtering SNP data

Introduction

Next-generation Sequencing (NGS) is one of the fundamental technological developments of the decade in life sciences. Whole Genome Sequencing (WGS), RAD-Seq, RNA-Seq, Chip-Seq, and several other technologies are routinely used to investigate important biological problems. These are also called high-throughput sequencing technologies with good reason: they generate vast amounts of data that need to be processed. ...