make ani default

sourmash-bio · Feb 24, 2024 · 98cbc27 · 98cbc27
1 parent 1b64a53
commit 98cbc27
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/src/python/sourmash_plugin_branchwater/__init__.py b/src/python/sourmash_plugin_branchwater/__init__.py
@@ -366,10 +366,10 @@ def __init__(self, p):
                        help='output csv file for the clusters')
         p.add_argument('--cluster-sizes', required=True,
                        help='output file for the cluster size histogram')
-        p.add_argument('--similarity-column', type=str, default='containment',
+        p.add_argument('--similarity-column', type=str, default='average_ani',
                           choices=['containment', 'max_containment', 'jaccard', 'average_ani', 'max_ani'],
                           help='column to use as distance measure')
-        p.add_argument('-t', '--threshold',  type=float, default=0.5)
+        p.add_argument('-t', '--threshold',  type=float, default=95, help="similarity threshold for clustering. Default: 95% ANI")
         p.add_argument('-c', '--cores', default=0, type=int,
                        help='number of cores to use (default is all available)')