diff --git a/workflow/rules/aatrnaseq-process.smk b/workflow/rules/aatrnaseq-process.smk
index b2eb390..612f6b2 100644
--- a/workflow/rules/aatrnaseq-process.smk
+++ b/workflow/rules/aatrnaseq-process.smk
@@ -125,6 +125,7 @@ rule bwa_align:
     input:
         reads=get_alignment_fastq,
         idx=rules.bwa_idx.output,
+        ref_dict=rules.ref_dict.output,
     output:
         bam=maybe_temp(
             os.path.join(outdir, "bam", "aln", "{sample}", "{sample}.aln.bam")
@@ -144,6 +145,16 @@ rule bwa_align:
         | samtools view -F 20 -Sb - \
         | samtools sort -m 2G -@ 4 -o {output.bam}
 
+    # Embed reference M5 checksums into BAM header
+    {{
+        samtools view -H {output.bam} | head -1
+        grep '^@SQ' {input.ref_dict}
+        samtools view -H {output.bam} | grep -v -e '^@SQ' -e '^@HD' || true
+    }} > {output.bam}.header.sam
+    samtools reheader --no-PG {output.bam}.header.sam {output.bam} > {output.bam}.reheader
+    mv {output.bam}.reheader {output.bam}
+    rm {output.bam}.header.sam
+
     samtools index {output.bam}
     """
 
diff --git a/workflow/rules/aatrnaseq-reference.smk b/workflow/rules/aatrnaseq-reference.smk
index f09bcbf..792b07e 100644
--- a/workflow/rules/aatrnaseq-reference.smk
+++ b/workflow/rules/aatrnaseq-reference.smk
@@ -236,3 +236,19 @@ rule trim_reference:
             --adapter-3p "{params.adapter_3p}" \
             2>&1 | tee {log}
         """
+
+
+rule ref_dict:
+    """
+    Generate sequence dictionary with MD5 checksums for embedding in BAM headers.
+    """
+    input:
+        get_validated_reference(),
+    output:
+        os.path.join(outdir, "reference", "reference.dict"),
+    log:
+        os.path.join(outdir, "logs", "reference", "dict.log"),
+    shell:
+        """
+        samtools dict {input} -o {output} 2> {log}
+        """