diff --git a/VERSIONLOG.md b/VERSIONLOG.md
index b3ec3686..4b566065 100644
--- a/VERSIONLOG.md
+++ b/VERSIONLOG.md
@@ -1,5 +1,8 @@
 # TACA Version Log
 
+## 20210716.1
+Handle special case with index 2 only for NovaSeq
+
 ## 20210617.1
 Support addtional 10X index types
 
diff --git a/taca/illumina/HiSeqX_Runs.py b/taca/illumina/HiSeqX_Runs.py
index 812cf4a9..4458e474 100755
--- a/taca/illumina/HiSeqX_Runs.py
+++ b/taca/illumina/HiSeqX_Runs.py
@@ -263,7 +263,7 @@ def _generate_per_lane_base_mask(self, sample_type, mask_table):
             index1_size = lane_contents[0]
             index2_size = lane_contents[1]
             is_dual_index = False
-            if index1_size != 0 and index2_size != 0:
+            if (index1_size != 0 and index2_size != 0) or (index1_size == 0 and index2_size != 0):
                 is_dual_index = True
             # Compute the basemask
             base_mask = self._compute_base_mask(runSetup, sample_type, index1_size, is_dual_index, index2_size)