Bioinformatics with Python Cookbook
I would like to announce my new book:
This book is slightly different from the standard books on Bioinformatics and Python.
It is not about teaching Bioinformatics algorithms, but about solving practical day-to-day problems with Python, for example:
- Next-Generation Sequencing: FASTQ, BAM and VCF processing. Along with filtering of datasets
- Genomics: processing reference genomes of both high-quality references of model species and low-quality non-model species. Also discussed are genome annotations and gene ontologies
- Population Genetics: doing PCA, Admixture/Structure, computing FSTs, ...
- Genome simulation: mostly forward-time simulations, but also a bit of coalescent
- Phylogenetics: tree reconstruction and tree drawing
- Proteins: PDB processing and visualization.
- Other topics like processing map data, GBIF, interfacing with Cytoscape, accessing lots of online databases, ...
- There is a bit on interacting with R/Bioconductor via Python
- Finally we discuss high-performance in Python: faster algorithms, clusters, Numba and Cython. Also related technologies like Docker
The book discusses the usual Python Libraries in the field: Biopython, PyVCF, Pysam, simuPOP, DendroPy, Pymol and also scientific libraries like NumPy, SciPy, matplotlib and scikit-learn.
The code is fully available for free at github. I am keen on maintaining the book code, so if you find any issues please do contact me.
The book is available in the usual places (Amazon, ...).