diff --git a/scripts/reverse_reversed_sequences.py b/scripts/reverse_reversed_sequences.py
deleted file mode 100644
index f838a20d..00000000
--- a/scripts/reverse_reversed_sequences.py
+++ /dev/null
@@ -1,32 +0,0 @@
-import pandas as pd
-import argparse
-from Bio import SeqIO
-
-if __name__=="__main__":
-    parser = argparse.ArgumentParser(
-        description="Reverse-complement reverse-complemented sequence",
-        formatter_class=argparse.ArgumentDefaultsHelpFormatter
-    )
-
-    parser.add_argument('--metadata', type=str, required=True, help="input metadata")
-    parser.add_argument('--sequences', type=str, required=True, help="input sequences")
-    parser.add_argument('--output', type=str, required=True, help="output sequences")
-    args = parser.parse_args()
-
-    metadata = pd.read_csv(args.metadata, sep='\t')
-    
-    # Read in fasta file
-    with open(args.sequences, 'r') as f_in:
-        with open(args.output, 'w') as f_out:
-            for seq in SeqIO.parse(f_in, 'fasta'):
-                # Check if metadata['reverse'] is True
-                try:
-                    if metadata.loc[metadata['strain'] == seq.id, 'reverse'].values[0] == True:
-                        # Reverse-complement sequence
-                        seq.seq = seq.seq.reverse_complement()
-                        print("Reverse-complementing sequence:", seq.id)
-                except:
-                    print("No reverse complement for:", seq.id)
-                    
-                # Write sequences to file
-                SeqIO.write(seq, f_out, 'fasta')
diff --git a/workflow/snakemake_rules/core.smk b/workflow/snakemake_rules/core.smk
index 77299730..d80801d0 100644
--- a/workflow/snakemake_rules/core.smk
+++ b/workflow/snakemake_rules/core.smk
@@ -102,21 +102,6 @@ rule combine_samples:
         """
 
 
-rule separate_reverse_complement:
-    input:
-        metadata=build_dir + "/{build_name}/metadata.tsv",
-        sequences=build_dir + "/{build_name}/filtered.fasta",
-    output:
-        build_dir + "/{build_name}/reversed.fasta",
-    shell:
-        """
-        python3 scripts/reverse_reversed_sequences.py \
-            --metadata {input.metadata} \
-            --sequences {input.sequences} \
-            --output {output}
-        """
-
-
 rule align:
     message:
         """
@@ -124,7 +109,7 @@ rule align:
           - filling gaps with N
         """
     input:
-        sequences=rules.separate_reverse_complement.output,
+        sequences=rules.combine_samples.output.sequences,
         reference=config["reference"],
         genemap=config["genemap"],
     output:
@@ -142,7 +127,6 @@ rule align:
             --genemap {input.genemap} \
             --max-indel {params.max_indel} \
             --seed-spacing {params.seed_spacing} \
-            --retry-reverse-complement \
             --output-fasta - \
             --output-insertions {output.insertions} \
             {input.sequences} | seqkit seq -i > {output.alignment}