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Welcome to kmerExtractor's documentation!
=========================================

A genome sequence is composed of four basic types of nucleotides: adenine (A), cytosine (C), guanine (G), and thymine (T).
All possible nucleotide substrings of length k are called **k-mers**. For example, for :math:`k=2` there are :math:`4^k=4^2=16` different 2-mers corresponding to: AA, AC, AG, AT, CA, CC, CG, CT, GA, GC, GG, GT, TA, TC, TG, TT.

The kmerExtractor software calculates the k-mer frequencies for windows within the chromosomes of an organism's sequence.
It takes as input a FASTA file with the nucleotide sequence of an organism separated by chromosomes. The software splits the chromosomes into windows of the size specified by the user. For a given :math:`k`, the kmerExtractor computes the frequency of the k-mers in the different windows within the chromosomes. It returns a csv file indicating the chromosome, the window index, the start and end position of the window, and the frequencies of the corresponding k-mers.

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   modules
   kmerExtractorTutorial

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`