SATAY Tools Documentation
=========================

SATAY Tools is a Python package for analyzing SATAY (Saturation Transposon Analysis in Yeast) 
transposon insertion sequencing data. This tool provides utilities for processing transposon 
mutagenesis datasets, including read mapping, insertion site identification, and downstream 
analysis of yeast fitness data.


Features
--------

- Process FASTQ files from transposon sequencing experiments
- Map transposon insertion sites to yeast genome
- Count and analyze insertion frequencies
- Perform differential analysis of insertion patterns


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

   installation
   quickstart
   tutorials/index
   api/index
   changelog



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

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