pysequila's documentation
=========================

PySeQuiLa is a Python wrapper for SeQuiLa,
an ANSI-SQL compliant solution for distributed processing of Next Generation Sequencing data built on top of Apache Spark.
PySeQuiLa extends Apache Spark SQL with highly efficient implementations of common bioinformatics operations such as
interval joins, depth of coverage or pileup (see `Algorithms <http://biodatageeks.org/sequila/architecture/architecture.html#methods>`_ and
`Benchmarks <https://pysequila.biodatageeks.org/doc/snapshot/benchmarking/benchmarking.html>`_).
It combines analytical power of Python with SQL syntax for almost unlimited querying and processing of NGS data.

For any topics not covered here please refer to `SeQuiLa documentation <http://biodatageeks.org/sequila/>`_

Contents:

.. toctree::
   :maxdepth: 1

   notebooks/pysequila/doc/quick_start.ipynb
   notebooks/pysequila/doc/initialize.ipynb
   notebooks/pysequila/doc/file_formats.ipynb
   notebooks/pysequila/doc/genomic_intervals.ipynb
   notebooks/pysequila/doc/coverage_analysis.ipynb
   notebooks/pysequila/doc/pileup_analysis.ipynb
   notebooks/pysequila/doc/kubernetes.ipynb
   benchmarking/benchmarking
   citation/citation

.. toctree::
   :maxdepth: 1