BioNumPy

Getting started

• What is BioNumPy?
• Installation and getting started
• Your first BioNumPy program

BioNumPy concepts

• Reading files
  • Method 1: Reading all your data at once
  • Method 2: Reading a single chunk from a large file
  • Method 3: Reading whole file as a stream of chunks
• Working with big data
• Currently supported file formats
  • Example
• Implementing a new file format
• Sequences
• Broadcastable Functions
  • Elementwise broadcasting in numpy
  • Vectorwise broadcasting
  • Sequence broadcasting
• Rollable Functions
• Summarization

Tutorials

• BAM Handling
• FASTQ filtering
• Simple quality checking of fastq files
• Using Numpy Functionality
• Position Weight Matrix

Other

• Contributing