From f55f64a14b6b334dedc44b57c6f84c2a1d2e6a39 Mon Sep 17 00:00:00 2001 From: Sergey Koren Date: Wed, 13 Jul 2016 13:33:41 -0400 Subject: [PATCH] Update quickstart.rst --- docs/source/quickstart.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/source/quickstart.rst b/docs/source/quickstart.rst index 616af0d..9d189ed 100644 --- a/docs/source/quickstart.rst +++ b/docs/source/quickstart.rst @@ -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. `_. 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.