.. _fasta: https://en.wikipedia.org/wiki/FASTA_format
.. _fastq: https://en.wikipedia.org/wiki/FASTQ_format
.. _BLAT: http://genome.ucsc.edu/cgi-bin/hgBlat
.. _KMA: https://bitbucket.org/genomicepidemiology/kma/src/master/
.. _BWA: https://bio-bwa.sourceforge.net/


.. _api:

.. toctree::
    :glob:

=================
API Documentation
=================

.. automodule:: pymlst

Whole Genome MLST
-----------------

.. automodule:: pymlst.wg.core
    :members:
    :member-order: bysource

.. automodule:: pymlst.wg.extractors
    :members:
    :member-order: bysource

Classical MLST
-----------------

.. automodule:: pymlst.cla.core
    :members:
    :member-order: bysource

Other Typing
-----------------

.. automodule:: pymlst.pytyper.core
    :members:
    :member-order: bysource