kPAL
latest
  • Introduction
  • Installation
  • Methodology
  • Tutorial
  • Using the Python library
  • API reference
  • Development
  • k-mer profile file format
  • Changelog
  • Copyright
kPAL
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  • Welcome to kPAL (k-mer profile analysis library)!
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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
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© Copyright 2013-2014, LUMC, Jeroen F.J. Laros, Martijn Vermaat. Revision 79b2ff97.

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