Working with modern sequence formats

Here, we will work with FASTQ files, the standard format output used by modern sequencers. You will learn how to work with quality scores per base and also consider 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 1,000 Genomes Project. We will start with a brief description of the project.

Getting ready

The human 1,000 Genomes Project aims to catalog worldwide 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 “1,000 Genomes” is actually a misnomer, because it currently includes more than 2,500 samples. These samples are divided into hundreds of populations, spanning the whole planet. We will mostly use data from four populations...