Working with modern sequence formats

Here, we will work with FASTQ files, the standard format output by modern sequencers. You will learn how to work with quality scores per base and also consider the variations in output coming from different sequencing machines and databases. This is the first recipe that will use real data (big data) from the human 1000 genomes project. We will start with a brief description of the project.

Getting ready

The human 1000 genomes project aims to catalog world-wide human genetic variation and takes advantage of modern sequencing technology to do WGS. This project makes all data publicly available, which includes output from sequencers, sequence alignments, and SNP calls, among many other artifacts. The name 1000 genomes is actually a misnomer because it currently includes more than 2500 samples. These samples are divided into 26 populations, spanning the whole planet. We will mostly use data from four populations: African Yorubans (YRI), Utah Residents with...