diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
index e548ded..f237afb 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
@@ -309,7 +309,7 @@
      *            : next neighbor in gene-code format
      * @return the merged Kmer, this K of this Kmer is k+1
      */
-    public void mergeKmerWithNextCode(byte nextCode) {
+    public void mergeNextCode(byte nextCode) {
         this.kmerlength += 1;
         setSize(KmerUtil.getByteNumFromK(kmerlength));
         if (kmerlength % 4 == 1) {
@@ -318,7 +318,48 @@
             }
             bytes[offset] = (byte) (nextCode & 0x3);
         } else {
-            bytes[offset] = (byte) (bytes[offset] | ((nextCode & 0x3) << (((kmerlength-1) % 4) << 1)));
+            bytes[offset] = (byte) (bytes[offset] | ((nextCode & 0x3) << (((kmerlength - 1) % 4) << 1)));
+        }
+        clearLeadBit();
+    }
+
+    /**
+     * Merge Kmer with the next connected Kmer
+     * e.g. AAGCTAA merge with AACAACC, if the initial kmerSize = 3
+     * then it will return AAGCTAACAACC
+     * 
+     * @param initialKmerSize
+     *            : the initial kmerSize
+     * @param kmer
+     */
+    @SuppressWarnings("unchecked")
+    public void mergeNextKmer(int initialKmerSize, KmerBytesWritable kmer) {
+        if (kmer.getKmerLength() == initialKmerSize){
+            mergeNextCode(kmer.getGeneCodeAtPosition(kmer.getKmerLength()-1));
+            return;
+        }
+        int preKmerLength = kmerlength;
+        int preSize = size;
+        this.kmerlength += kmer.kmerlength - initialKmerSize + 1;
+        setSize(KmerUtil.getByteNumFromK(kmerlength));
+        int i = 1;
+        for (; i <= preSize; i++) {
+            bytes[offset + size - i] = bytes[offset + preSize - i];
+        }
+        if (i > 1) {
+            i--;
+        }
+        if (preKmerLength % 4 == 0) {
+            for (int j = 1; j <= kmer.getLength() && offset + size >= i + j; j++) {
+                bytes[offset + size - i - j] = kmer.getBytes()[kmer.getOffset() + kmer.getLength() - j];
+            }
+        } else {
+            int posNeedToMove = ((preKmerLength % 4) << 1);
+            bytes[offset + size - i] |= kmer.getBytes()[kmer.getOffset() + kmer.getLength() - 1] << posNeedToMove;
+            for (int j = 1; j <= kmer.getLength() && offset + size - i - j >= 0; j++) {
+                bytes[offset + size - i - j] = (byte) (((kmer.getBytes()[kmer.getOffset() + kmer.getLength() - j] & 0xff) >> (8 - posNeedToMove)) | (kmer
+                        .getBytes()[kmer.getOffset() + kmer.getLength() - j - 1] << posNeedToMove));
+            }
         }
         clearLeadBit();
     }
@@ -391,4 +432,5 @@
     static { // register this comparator
         WritableComparator.define(KmerBytesWritable.class, new Comparator());
     }
+
 }
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
index 0276c3a..daf4a4f 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
@@ -16,8 +16,8 @@
     private PositionListWritable incomingList;
     private PositionListWritable outgoingList;
     private KmerBytesWritable kmer;
-    
-    public NodeWritable(){
+
+    public NodeWritable() {
         nodeID = new PositionWritable();
         incomingList = new PositionListWritable();
         outgoingList = new PositionListWritable();
@@ -31,10 +31,6 @@
         kmer = new KmerBytesWritable(kmerSize);
     }
 
-    public int getCount() {
-        return kmer.getKmerLength();
-    }
-
     public void setNodeID(PositionWritable ref) {
         this.setNodeID(ref.getReadID(), ref.getPosInRead());
     }
@@ -74,9 +70,13 @@
         return kmer;
     }
 
-    public void mergeNextWithinOneRead(NodeWritable nextNodeEntry) {
-        this.outgoingList.set(nextNodeEntry.outgoingList);
-        kmer.mergeKmerWithNextCode(nextNodeEntry.kmer.getGeneCodeAtPosition(nextNodeEntry.getCount() - 1));
+    public int getCount() {
+        return kmer.getKmerLength();
+    }
+
+    public void mergeNext(NodeWritable nextNode, int initialKmerSize) {
+        this.outgoingList.set(nextNode.outgoingList);
+        kmer.mergeNextKmer(initialKmerSize, nextNode.getKmer());
     }
 
     public void set(NodeWritable node) {
@@ -111,9 +111,9 @@
     public int hashCode() {
         return nodeID.hashCode();
     }
-    
+
     @Override
-    public String toString(){
+    public String toString() {
         StringBuilder sbuilder = new StringBuilder();
         sbuilder.append('(');
         sbuilder.append(nodeID.toString()).append('\t');
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
index b7dd8f1..04fc3bb 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
@@ -59,7 +59,7 @@
         Assert.assertEquals(kmer.toString(), "AATAGAA");
 
         kmer.setByReadReverse(array, 1);
-        Assert.assertEquals(kmer.toString(), "GAAGATA");
+        Assert.assertEquals(kmer.toString(), "CTTCTAT");
     }
 
     @Test
@@ -100,11 +100,35 @@
         String text = "AGCTGACCG";
         for (int i = 0; i < 10; i++) {
             for (byte x = GeneCode.A; x <= GeneCode.T; x++) {
-                kmer.mergeKmerWithNextCode(x);
+                kmer.mergeNextCode(x);
                 text = text + (char) GeneCode.GENE_SYMBOL[x];
                 Assert.assertEquals(text, kmer.toString());
             }
         }
     }
+    
+    @Test
+    public void TestMergeNextKmer(){
+        byte[] array = { 'A', 'G', 'C', 'T', 'G', 'A', 'C', 'C', 'G', 'T' };
+        KmerBytesWritable kmer1 = new KmerBytesWritable(9);
+        kmer1.setByRead(array, 0);
+        String text1 = "AGCTGACCG";
+        KmerBytesWritable kmer2 = new KmerBytesWritable(9);
+        kmer2.setByRead(array, 1);
+        String text2 = "GCTGACCGT";
+        Assert.assertEquals(text1, kmer1.toString());
+        Assert.assertEquals(text2, kmer2.toString());
+
+        KmerBytesWritable merged = new KmerBytesWritable(kmer1);
+        merged.mergeNextKmer(9, kmer2);
+        Assert.assertEquals("AGCTGACCGT", merged);
+
+        KmerBytesWritable kmer3 = new KmerBytesWritable(3);
+        kmer3.setByRead(array, 1);
+        String text3 = "GCT";
+        Assert.assertEquals(text3, kmer3.toString());
+        merged.mergeNextKmer(1, kmer3);
+        Assert.assertEquals(text1 + text3, merged.toString());
+    }
 
 }
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java
index d81c595..d80ed13 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java
@@ -115,7 +115,7 @@
 
                 if (nextNodeEntry.getOutgoingList().getCountOfPosition() == 0) {
                     if (pNextNext == null || pNextNext.getOutgoingList().getCountOfPosition() == 0) {
-                        curNodeEntry.mergeNextWithinOneRead(nextNodeEntry);
+                        curNodeEntry.mergeNext(nextNodeEntry, kmerSize);
                     } else {
                         curNodeEntry.getOutgoingList().reset();
                         curNodeEntry.getOutgoingList().append(nextNodeEntry.getNodeID());