diff --git a/circlator/common.py b/circlator/common.py
index 1a03374..6f2de32 100644
--- a/circlator/common.py
+++ b/circlator/common.py
@@ -1,7 +1,7 @@
 import sys
 import subprocess
 
-version = '0.12.1'
+version = '0.13.0'
 
 def syscall(cmd, allow_fail=False, verbose=False):
     if verbose:
diff --git a/circlator/merge.py b/circlator/merge.py
index 7acbbdb..8a2dab9 100644
--- a/circlator/merge.py
+++ b/circlator/merge.py
@@ -15,6 +15,7 @@ def __init__(
           reassembly,
           outprefix,
           reads=None,
+          nucmer_diagdiff=25,
           nucmer_min_id=95,
           nucmer_min_length=500,
           nucmer_min_length_for_merges=4000,
@@ -34,6 +35,7 @@ def __init__(
         self.reassembly_fasta = reassembly
         self.reads = reads
         self.outprefix = outprefix
+        self.nucmer_diagdiff = nucmer_diagdiff
         self.nucmer_min_id = nucmer_min_id
         self.nucmer_min_length = nucmer_min_length
         self.nucmer_min_length_for_merges = nucmer_min_length_for_merges
@@ -59,6 +61,7 @@ def _run_nucmer(self, ref, qry, outfile):
             outfile,
             min_id=self.nucmer_min_id,
             min_length=self.nucmer_min_length,
+            diagdiff=self.nucmer_diagdiff,
             maxmatch=True,
             breaklen=self.nucmer_breaklen,
             simplify=False,
diff --git a/circlator/tasks/all.py b/circlator/tasks/all.py
index 98a8d3a..40fff13 100644
--- a/circlator/tasks/all.py
+++ b/circlator/tasks/all.py
@@ -32,6 +32,7 @@ def run():
     #assemble_group = parser.add_argument_group('assemble_group')
 
     merge_group = parser.add_argument_group('merge options')
+    merge_group.add_argument('--merge_diagdiff', type=int, help='Nucmer diagdiff option [%(default)s]', metavar='INT', default=25)
     merge_group.add_argument('--merge_min_id', type=float, help='Nucmer minimum percent identity [%(default)s]', metavar='FLOAT', default=95)
     merge_group.add_argument('--merge_min_length', type=int, help='Minimum length of hit for nucmer to report [%(default)s]', metavar='INT', default=500)
     merge_group.add_argument('--merge_min_length_merge', type=int, help='Minimum length of nucmer hit to use when merging [%(default)s]', metavar='INT', default=4000)
@@ -122,6 +123,7 @@ def run():
         original_assembly,
         reassembly,
         merge_prefix,
+        nucmer_diagdiff=options.merge_diagdiff,
         nucmer_min_id=options.merge_min_id,
         nucmer_min_length=options.merge_min_length,
         nucmer_min_length_for_merges=options.merge_min_length_merge,
diff --git a/circlator/tasks/merge.py b/circlator/tasks/merge.py
index 904cbcc..b912ced 100644
--- a/circlator/tasks/merge.py
+++ b/circlator/tasks/merge.py
@@ -7,6 +7,7 @@ def run():
         usage = 'circlator merge [options] <original.fasta> <new.fasta> <outprefix>'
     )
 
+    parser.add_argument('--diagdiff', type=int, help='Nucmer diagdiff option [%(default)s]', metavar='INT', default=25)
     parser.add_argument('--min_id', type=float, help='Nucmer minimum percent identity [%(default)s]', metavar='FLOAT', default=95)
     parser.add_argument('--min_length', type=int, help='Minimum length of hit for nucmer to report [%(default)s]', metavar='INT', default=500)
     parser.add_argument('--min_length_merge', type=int, help='Minimum length of nucmer hit to use when merging [%(default)s]', metavar='INT', default=4000)
@@ -26,6 +27,7 @@ def run():
         options.original_assembly,
         options.new_assembly,
         options.outprefix,
+        nucmer_diagdiff=options.diagdiff,
         nucmer_min_id=options.min_id,
         nucmer_min_length=options.min_length,
         nucmer_min_length_for_merges=options.min_length_merge,
diff --git a/setup.py b/setup.py
index 2fa2cbe..b1c4b16 100644
--- a/setup.py
+++ b/setup.py
@@ -7,7 +7,7 @@
 
 setup(
     name='circlator',
-    version='0.12.1',
+    version='0.13.0',
     description='circlator: a tool to circularise bacterial genome assemblies',
     packages = find_packages(),
     package_data={'circlator': ['data/*']},
@@ -21,8 +21,8 @@
         'openpyxl',
         'pyfastaq >= 3.5.0',
         'pysam >= 0.8.1',
-        'pymummer>=0.2.0',
-        'bio_assembly_refinement>=0.1.0',
+        'pymummer>=0.4.0',
+        'bio_assembly_refinement>=0.3.2',
     ],
     license='GPLv3',
     classifiers=[