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Update quickstart.rst
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skoren authored Jul 13, 2016
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Expand Up @@ -35,11 +35,13 @@ means the k-mer GGGGGGGGGGG represents 0.05% of the k-mers in the dataset (so if
It is also possible to use the k-mer list as a positive selection as was used in `Carvalho et. al. <http://biorxiv.org/content/biorxiv/early/2016/05/14/053256.full.pdf>`_. Specify the k-mer list as above and the flag:

.. code-block:: bash
--supress-noise 2
which will not allow any k-mer not in in the input file to be a minmer. The k-mers above --filter-threshold will be ignored as repeats.

.. code-block:: bash
--supress-noise 1
will downweight any k-mer not in the input file to bias against its selection as a minmer. The k-mers above --filter-threshold will be downeighted as repeats.
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