Meryl
=====

.. toctree::
   :hidden:

   quick-start
   faq
   tutorial
   reference
   history


`Meryl <http://github.com/marbl/meryl>`_ is a k-mer counting and processing tool.

Publications
============

Rhie A, Walenz BP, Koren S, Phillippy AM.
`Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies <https://doi.org/10.1186/s13059-020-02134-9>`_. Genome Biology 21, 245 (2020).

Install
=======
The easiest way to get started is to download a `release <https://github.com/marbl/meryl/releases>`_. If you encounter
any issues, please report them using the `github issues <http://github.com/marbl/meryl/issues>`_ page.

Alternatively, you can also build the latest unreleased from github:

::

  git clone https://github.com/marbl/meryl.git
  cd meryl/src
  make -j <number of threads>

Learn
=====

*  :ref:`Quick Start             <quick-start>` - no experience or data required, download and analyze *Escherichia coli* repeats today!
*  :ref:`Tutorial and Examples   <tutorial>`    - a more in-depth look at the meryl command
*  :ref:`Parameter Reference     <reference>`   - alphabetical list of meryl actions
*  :ref:`History                 <history>`     - the history of meryl
*  :ref:`FAQ                     <faq>`         - Frequently asked questions
