Welcome to kPAL (k-mer profile analysis library)!

kPAL is an analysis toolkit and Python programming library for k-mer profiles.

Note

Please cite the following paper if you use kPAL in your own work:

Anvar et al., Determining the quality and complexity of next-generation sequencing data without a reference genome. Genome Biology 2014, 15:555. doi:10.1186/s13059-014-0555-3

User’s guide

• Introduction
• Installation
  • Dependencies
  • Latest kPAL release
  • kPAL development version
• Methodology
  • k-mer counting
  • Distance metrics
  • Strand balance
  • Profile shrinking
  • Scaling and smoothing
• Tutorial
  • k-mer counting
  • Merging profiles
  • Distance between profiles
  • Enforcing strand balance
  • Custom merge functions
• Using the Python library
  • k-mer profiles
  • Storing k-mer profiles
  • Differences between k-mer profiles

API reference

• API reference
  • k-mer profiles
  • k-mer profile distances
  • Metrics

Additional notes

• Development
  • Contributing
  • Documentation
  • Unit tests
  • Coding style
  • Versioning
• k-mer profile file format
  • Versioning
  • Current version: 1.0.0
  • Changes from older versions
• Changelog
  • Version 2.1.2
  • Version 2.1.1
  • Version 2.1.0
  • Version 2.0.1
  • Version 2.0.0
  • Version 1.0.1
  • Version 1.0.0
  • Version 0.3.0
  • Version 0.2.0
  • Version 0.1.0
• Copyright
  • Authors
  • License
  • Citations

Indices and tables

• Index
• Module Index
• Search Page