diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java
index bbc1618ac..ab6b17c35 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java
@@ -50,6 +50,7 @@ import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.walkers.haplotypecaller.KMerCounter;
 import org.broadinstitute.sting.gatk.walkers.haplotypecaller.Kmer;
 import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.*;
+import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.collections.PrimitivePair;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@@ -611,7 +612,7 @@ public class ReadThreadingGraph extends BaseGraph<MultiDeBruijnVertex, MultiSamp
 
         int lastGood = -1; // the index of the last good base we've seen
         for( int end = 0; end <= sequence.length; end++ ) {
-            if ( end == sequence.length || qualities[end] < minBaseQualityToUseInAssembly ) {
+            if ( end == sequence.length || ! baseIsUsableForAssembly(sequence[end], qualities[end]) ) {
                 // the first good base is at lastGood, can be -1 if last base was bad
                 final int start = lastGood;
                 // the stop base is end - 1 (if we're not at the end of the sequence)
@@ -631,6 +632,18 @@ public class ReadThreadingGraph extends BaseGraph<MultiDeBruijnVertex, MultiSamp
         }
     }
 
+    /**
+     * Determines whether a base can safely be used for assembly.
+     * Currently disallows Ns and/or those with low quality
+     *
+     * @param base  the base under consideration
+     * @param qual  the quality of that base
+     * @return true if the base can be used for assembly, false otherwise
+     */
+    protected boolean baseIsUsableForAssembly(final byte base, final byte qual) {
+        return base != BaseUtils.Base.N.base && qual >= minBaseQualityToUseInAssembly;
+    }
+
     /**
      * Get the set of non-unique kmers in this graph.  For debugging purposes
      * @return a non-null set of kmers
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java
index 74361de1b..a74ce1c75 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java
@@ -251,7 +251,7 @@ public class LocalAssemblyEngineUnitTest extends BaseTest {
             for ( int snpPos = 0; snpPos < windowSize; snpPos++) {
                 if ( snpPos > excludeVariantsWithXbp && (windowSize - snpPos) >= excludeVariantsWithXbp ) {
                     final byte[] altBases = ref.getBytes();
-                    altBases[snpPos] = 'N';
+                    altBases[snpPos] = altBases[snpPos] == 'A' ? (byte)'C' : (byte)'A';
                     final String alt = new String(altBases);
                     tests.add(new Object[]{"SNP at " + snpPos, assembler, refLoc, ref, alt});
                 }
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java
index 340777513..67ee52734 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java
@@ -48,10 +48,8 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading;
 
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.walkers.haplotypecaller.Kmer;
-import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.MultiSampleEdge;
-import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.SeqGraph;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.*;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.haplotype.Haplotype;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
@@ -180,7 +178,31 @@ public class ReadThreadingGraphUnitTest extends BaseTest {
         Assert.assertFalse(rtgraph75.hasCycles());
     }
 
-    // TODO -- update to use determineKmerSizeAndNonUniques directly
+    @Test(enabled = !DEBUG)
+    public void testNsInReadsAreNotUsedForGraph() {
+
+        final int length = 100;
+        final byte[] ref = Utils.dupBytes((byte)'A', length);
+
+        final ReadThreadingGraph rtgraph = new ReadThreadingGraph(25);
+        rtgraph.addSequence("ref", ref, null, true);
+
+        // add reads with Ns at any position
+        for ( int i = 0; i < length; i++ ) {
+            final byte[] bases = ref.clone();
+            bases[i] = 'N';
+            final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(bases, Utils.dupBytes((byte) 30, length), length + "M");
+            rtgraph.addRead(read);
+        }
+        rtgraph.buildGraphIfNecessary();
+
+        final SeqGraph graph = rtgraph.convertToSequenceGraph();
+        final KBestPaths<SeqVertex,BaseEdge> pathFinder = new KBestPaths<>(false);
+        Assert.assertEquals(pathFinder.getKBestPaths(graph, length, graph.getReferenceSourceVertex(), graph.getReferenceSinkVertex()).size(), 1);
+    }
+
+
+// TODO -- update to use determineKmerSizeAndNonUniques directly
 //    @DataProvider(name = "KmerSizeData")
 //    public Object[][] makeKmerSizeDataProvider() {
 //        List<Object[]> tests = new ArrayList<Object[]>();