Bioinformatics with Python Cookbook - Second Edition

Getting ready

You will need to get the metadata file from the 1,000 Genomes sequence index. Please check https://github.com/PacktPublishing/Bioinformatics-with-Python-Cookbook-Second-Edition/blob/master/Datasets.ipynb and download the sequence.index file. If you are using Jupyter Notebook, open the Chapter01/Interfacing_R.ipynb file and just execute the wget command on top.

This file has information about all of the FASTQ files in the project (we will use data from the Human 1,000 Genomes Project in the chapters to come). This includes the FASTQ file, the sample ID, and the population of origin, and important statistical information per lane, such as the number of reads and number of DNA bases read.