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You're reading from Bioinformatics with Python Cookbook Learn how to use modern Python bioinformatics libraries and applications to do cutting-edge research in computational biology

Product type Paperback

Published in Nov 2018

Publisher Packt

ISBN-13 9781789344691

Length 360 pages

Edition 2nd Edition

Languages

Python

Tools

Biopython

Concepts

Bioinformatics

Author (1):

Tiago Antao

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Table of Contents (12) Chapters

Preface

1. Python and the Surrounding Software Ecology

2. Next-Generation Sequencing FREE CHAPTER

3. Working with Genomes

4. Population Genetics

5. Population Genetics Simulation

6. Phylogenetics

7. Using the Protein Data Bank

8. Bioinformatics Pipelines

9. Python for Big Genomics Datasets

10. Other Topics in Bioinformatics

11. Advanced NGS Processing

Python for Big Genomics Datasets

In this chapter, we will cover the following recipes:

Using high-performance data formats – HDF5
Doing parallel computing with Dask
Using high-performance data formats – Parquet
Computing sequencing statistics using Spark
Optimizing code with Cython and Numba

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Authors (1)

Tiago Antao

Tiago Antao is a bioinformatician currently working in the field of genomics. A former computer scientist, Tiago moved into computational biology with an MSc in Bioinformatics from the Faculty of Sciences at the University of Porto (Portugal) and a PhD on the spread of drug-resistant malaria from the Liverpool School of Tropical Medicine (UK). Postdoctoral, Tiago has worked with human datasets at the University of Cambridge (UK) and with mosquito whole genome sequencing data at the University of Oxford (UK), before helping to set up the bioinformatics infrastructure at the University of Montana. He currently works as a data engineer in the biotechnology field in Boston, MA. He is one of the co-authors of Biopython, a major bioinformatics package written in Python.

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