Book Image

Bioinformatics with Python Cookbook - Second Edition

By : Tiago Antao
Book Image

Bioinformatics with Python Cookbook - Second Edition

By: Tiago Antao

Overview of this book

Bioinformatics is an active research field that uses a range of simple-to-advanced computations to extract valuable information from biological data. This book covers next-generation sequencing, genomics, metagenomics, population genetics, phylogenetics, and proteomics. You'll learn modern programming techniques to analyze large amounts of biological data. With the help of real-world examples, you'll convert, analyze, and visualize datasets using various Python tools and libraries. This book will help you get a better understanding of working with a Galaxy server, which is the most widely used bioinformatics web-based pipeline system. This updated edition also includes advanced next-generation sequencing filtering techniques. You'll also explore topics such as SNP discovery using statistical approaches under high-performance computing frameworks such as Dask and Spark. By the end of this book, you'll be able to use and implement modern programming techniques and frameworks to deal with the ever-increasing deluge of bioinformatics data.
Table of Contents (16 chapters)
Title Page
About Packt
Contributors
Preface
Index

Working with alignment data


After you receive your data from the sequencer, you will normally use a tool such as Burrows-Wheeler Aligner (bwa) to align your sequences to a reference genome. Most users will have a reference genome for their species. You can read more on reference genomes in the next chapter, Chapter 3, Working with Genomes.

The most common representation for aligned data is the sequence alignment map (SAM) format. Due to the massive size of most of these files, you will probably work with its compressed version (BAM). The compressed format is indexable for extremely fast random access (for example, to speedily find alignments to a certain part of a chromosome). Note that you will need to have an index for your BAM file, which is normally created by the tabix utility of SAMtools. SAMtools is probably the most widely-used tool for manipulating SAM/BAM files.

Getting ready

As discussed in the previous recipe, we will use data from the 1,000 Genomes Project. We will use the exome...