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updates documentation to reflect installation options
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Tom Smith committed Apr 22, 2016
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Expand Up @@ -7,28 +7,38 @@ This repository contains tools for dealing with Unique Molecular Identifiers (UM
UMIs are removed and appended to the read name. Any other barcode, for example a library barcode, is left on the read.

* dedup: Implements a number of different UMI deduplication schemes.
The recommended methods are `directional_adjecency` and `adjecency`. In general `directional_adjecency` seems to be less sensitive to starting conditions, but there are situations where `adjacency` might out perform.
The recommended method is `directional_adjecency`.

See simulation results at the `CGAT blog <https://cgatoxford.wordpress.com/2015/08/14/unique-molecular-identifiers-the-problem-the-solution-and-the-proof/>`_.

`Genome Science 2015 poster <http://f1000research.com/posters/4-728>`_.

Preprint on the way shortly...


Installation
------------

Clone git repository:
If you're using Conda, you can use:

.. code:: bash
git clone [email protected]:CGATOxford/UMI-tools.git
conda install -c https://conda.anaconda.org/toms umi_tools
Enter repository and run:
Or pip:

.. code:: bash
python setup.py develop
pip install umi_tools
Or if you'd like to work directly from the git repository:

.. code:: bash
git clone [email protected]:CGATOxford/UMI-tools.git
Enter repository and run:

.. code:: bash
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