diff --git a/micall/core/denovo.py b/micall/core/denovo.py
index bed1f62a5..bf2362cfa 100644
--- a/micall/core/denovo.py
+++ b/micall/core/denovo.py
@@ -19,7 +19,7 @@
 from Bio.SeqRecord import SeqRecord
 
 from micall.core.project_config import ProjectConfig
-from micall.core.contig_stitcher import GenotypedContig
+from micall.core.contig_stitcher import GenotypedContig, stitch_consensus
 
 IVA = "iva"
 DEFAULT_DATABASE = os.path.join(os.path.dirname(__file__),
@@ -84,6 +84,7 @@ def write_contig_refs(contigs_fasta_path,
                          group_refs=group_refs)
 
     contigs = list(read_assembled_contigs(group_refs, genotypes, contigs_fasta_path))
+    contigs = list(stitch_consensus(contigs))
 
     for contig in contigs:
         writer.writerow(dict(ref=contig.ref_name,