diff --git a/reat.yml b/reat.yml
index 8c3d582..d1cb1fa 100644
--- a/reat.yml
+++ b/reat.yml
@@ -10,7 +10,6 @@ dependencies:
   - bioawk=1.0
   - seqkit=0.16.1
   - samtools=1.12
-  - mikado=2.3.3
   - portcullis=1.2.2
   - stringtie=2.1.5
   - hisat2=2.2.1
diff --git a/setup.py b/setup.py
index 8418bb7..d598d4f 100644
--- a/setup.py
+++ b/setup.py
@@ -39,7 +39,6 @@
         "biopython~=1.78",
         "mikado~=2.3.0",
         "pyfaidx~=0.5.8",
-        "numpy~=1.20.3",
         "jsonschema~=3.2.0",
         "pyyaml~=5.4.1",
         "parasail~=1.2.4",