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 26 populations, spanning the whole planet. We will mostly use data from four populations: African Yorubans (YRI), Utah Residents with Northern and Western European Ancestry (CEU), Japanese in Tokyo (JPT), and Han Chinese in Beijing (CHB). The reason we chose these specific populations is because they were the first ones that came from HapMap, an old project with similar goals. They used genotyping arrays to find out more about the quality of this subset. We will revisit the 1,000 Genomes, and HapMap projects in Chapter 4, Population Genetics.

If you use Jupyter Notebook, do not forget to download the data, as specified on the first cell of Chapter02/Working_with_FASTQ.ipynb. If not, download the SRR003265.filt.fastq.gz file, which is linked in https://github.com/PacktPublishing/Bioinformatics-with-Python-Cookbook-Second-Edition/blob/master/Datasets.ipynb. This is a fairly small file (27 MB) and represents part of the sequenced data of a Yoruban female (NA18489). If you refer to the 1,000 Genomes Project, you will see that the vast majority of FASTQ files are much bigger (up to two orders of magnitude bigger).

The processing of FASTQ sequence files will mostly be performed using Biopython.