diff --git a/tools/bowtie2/bowtie2_macros.xml b/tools/bowtie2/bowtie2_macros.xml
index 4d0d5d99911..fcebff02ed1 100644
--- a/tools/bowtie2/bowtie2_macros.xml
+++ b/tools/bowtie2/bowtie2_macros.xml
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.5.3</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">2.5.4</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <!-- Import this at the top of your command block and then
          define rg_auto_name. -->
     <token name="@define_read_group_helpers@">
diff --git a/tools/bowtie2/bowtie2_wrapper.xml b/tools/bowtie2/bowtie2_wrapper.xml
index d8994313b4d..38687739429 100644
--- a/tools/bowtie2/bowtie2_wrapper.xml
+++ b/tools/bowtie2/bowtie2_wrapper.xml
@@ -8,7 +8,7 @@
     </xrefs>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">bowtie2</requirement>
-        <requirement type="package" version="1.19.2">samtools</requirement>
+        <requirement type="package" version="1.20">samtools</requirement>
     </requirements>
     <version_command>bowtie2 --version</version_command>
     <command detect_errors="exit_code"><![CDATA[