diff --git a/.bumpversion.cfg b/.bumpversion.cfg
index 2a098f28..83b61bd3 100644
--- a/.bumpversion.cfg
+++ b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.5.3
+current_version = 3.5.4
 commit = True
 tag = True
 tag_name = {new_version}
diff --git a/.github/workflows/package-blobtoolkit.yml b/.github/workflows/package-blobtoolkit.yml
index d2b20e63..9a0822f7 100644
--- a/.github/workflows/package-blobtoolkit.yml
+++ b/.github/workflows/package-blobtoolkit.yml
@@ -1,6 +1,6 @@
 name: release-blobtoolkit
 env:
-  VERSION: 3.5.3
+  VERSION: 3.5.4
 
 on:
   push:
diff --git a/README.md b/README.md
index f04dcc15..cd67c18f 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-# BlobToolKit (v3.5.3)
+# BlobToolKit (v3.5.4)
 
 [![MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](https://opensource.org/licenses/MIT)
 [![DOI](https://zenodo.org/badge/150091036.svg)](https://zenodo.org/badge/latestdoi/150091036)
diff --git a/setup.py b/setup.py
index c5e81a80..730984fc 100644
--- a/setup.py
+++ b/setup.py
@@ -97,7 +97,7 @@ def read(*names, **kwargs):
 
 setup(
     name="blobtoolkit",  # Required
-    version="3.5.3",
+    version="3.5.4",
     description="blobtoolkit",  # Optional
     long_description="blobtoolkit",  # Optional
     long_description_content_type="text/markdown",
diff --git a/src/blobtools/lib/version.py b/src/blobtools/lib/version.py
index d81f7396..100d8d9c 100644
--- a/src/blobtools/lib/version.py
+++ b/src/blobtools/lib/version.py
@@ -1,4 +1,4 @@
 #!/usr/bin/env python3
 """blobtoolkit version."""
 
-__version__ = "blobtoolkit v3.5.3"
+__version__ = "blobtoolkit v3.5.4"
diff --git a/src/btk/lib/version.py b/src/btk/lib/version.py
index d81f7396..100d8d9c 100644
--- a/src/btk/lib/version.py
+++ b/src/btk/lib/version.py
@@ -1,4 +1,4 @@
 #!/usr/bin/env python3
 """blobtoolkit version."""
 
-__version__ = "blobtoolkit v3.5.3"
+__version__ = "blobtoolkit v3.5.4"
diff --git a/src/docker/Dockerfile b/src/docker/Dockerfile
index c4a64873..2a634bae 100644
--- a/src/docker/Dockerfile
+++ b/src/docker/Dockerfile
@@ -1,7 +1,7 @@
 FROM ubuntu:20.04
 LABEL maintainer="blobtoolkit@genomehubs.org"
 LABEL license="MIT"
-ARG VERSION=3.5.3
+ARG VERSION=3.5.4
 LABEL version=$VERSION
 ENV CONTAINER_VERSION=$VERSION
 
diff --git a/src/docker/api/Dockerfile b/src/docker/api/Dockerfile
index c2a31823..d4a6385f 100644
--- a/src/docker/api/Dockerfile
+++ b/src/docker/api/Dockerfile
@@ -1,7 +1,7 @@
 FROM alpine:3.15
 LABEL maintainer="blobtoolkit@genomehubs.org"
 LABEL license="MIT"
-ARG VERSION=3.5.3
+ARG VERSION=3.5.4
 LABEL version=$VERSION
 
 ENV CONTAINER_VERSION=$VERSION
diff --git a/src/docker/blobtools/Dockerfile b/src/docker/blobtools/Dockerfile
index 2a13adf1..f1fa4a43 100644
--- a/src/docker/blobtools/Dockerfile
+++ b/src/docker/blobtools/Dockerfile
@@ -1,7 +1,7 @@
 FROM ubuntu:20.04
 LABEL maintainer="blobtoolkit@genomehubs.org"
 LABEL license="MIT"
-ARG VERSION=3.5.3
+ARG VERSION=3.5.4
 LABEL version=$VERSION
 ENV CONTAINER_VERSION=$VERSION
 
diff --git a/src/docker/blobtools/env.yaml b/src/docker/blobtools/env.yaml
index 9cf09571..498a0bca 100644
--- a/src/docker/blobtools/env.yaml
+++ b/src/docker/blobtools/env.yaml
@@ -9,4 +9,4 @@ dependencies:
   - python==3.9.13
   - seqtk==1.3
   - pip:
-      - blobtoolkit==3.5.3
+      - blobtoolkit==3.5.4
diff --git a/src/docker/env.yaml b/src/docker/env.yaml
index 0ec376db..e2f23303 100644
--- a/src/docker/env.yaml
+++ b/src/docker/env.yaml
@@ -16,4 +16,4 @@ dependencies:
   - samtools==1.15.1
   - seqtk==1.3
   - pip:
-      - blobtoolkit==3.5.3
+      - blobtoolkit==3.5.4
diff --git a/src/docker/viewer/Dockerfile b/src/docker/viewer/Dockerfile
index 898ff802..ce6ad769 100644
--- a/src/docker/viewer/Dockerfile
+++ b/src/docker/viewer/Dockerfile
@@ -1,7 +1,7 @@
 FROM alpine:3.15
 LABEL maintainer="blobtoolkit@genomehubs.org"
 LABEL license="MIT"
-ARG VERSION=3.5.3
+ARG VERSION=3.5.4
 LABEL version=$VERSION
 
 ENV CONTAINER_VERSION=$VERSION
diff --git a/src/pipeline/lib/version.py b/src/pipeline/lib/version.py
index d81f7396..100d8d9c 100644
--- a/src/pipeline/lib/version.py
+++ b/src/pipeline/lib/version.py
@@ -1,4 +1,4 @@
 #!/usr/bin/env python3
 """blobtoolkit version."""
 
-__version__ = "blobtoolkit v3.5.3"
+__version__ = "blobtoolkit v3.5.4"
diff --git a/src/viewer/README.md b/src/viewer/README.md
index 6742488b..1b472809 100644
--- a/src/viewer/README.md
+++ b/src/viewer/README.md
@@ -1,4 +1,4 @@
-# BlobToolKit Viewer (v3.5.3)
+# BlobToolKit Viewer (v3.5.4)
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1134794.svg)](https://doi.org/10.5281/zenodo.1134794)