diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java
index 5cb3169..bfb1e64 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java
@@ -9,6 +9,7 @@
 
 import edu.uci.ics.genomix.pregelix.type.CheckMessage;
 import edu.uci.ics.genomix.pregelix.type.Message;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
 import edu.uci.ics.genomix.type.PositionListWritable;
 import edu.uci.ics.genomix.type.VKmerBytesWritable;
 
@@ -19,7 +20,7 @@
      * file stores the point to the file that stores the chains of connected DNA
      */
     private VKmerBytesWritable sourceVertexId;
-    private VKmerBytesWritable kmer;
+    private VKmerBytesWritable actualKmer;
     private AdjacencyListWritable neighberNode; //incoming or outgoing
     private PositionListWritable nodeIdList = new PositionListWritable();
     private float averageCoverage;
@@ -33,7 +34,7 @@
 
     public MessageWritable() {
         sourceVertexId = new VKmerBytesWritable();
-        kmer = new VKmerBytesWritable();
+        actualKmer = new VKmerBytesWritable();
         neighberNode = new AdjacencyListWritable();
         startVertexId = new VKmerBytesWritable();
         averageCoverage = 0;
@@ -45,7 +46,7 @@
     public MessageWritable(int kmerSize) {
         kmerlength = kmerSize;
         sourceVertexId = new VKmerBytesWritable(kmerSize);
-        kmer = new VKmerBytesWritable(0);
+        actualKmer = new VKmerBytesWritable(0);
 
         neighberNode = new AdjacencyListWritable(kmerSize);
         startVertexId = new VKmerBytesWritable(kmerSize);
@@ -62,9 +63,9 @@
             checkMessage |= CheckMessage.SOURCE;
             this.sourceVertexId.setAsCopy(msg.getSourceVertexId());
         }
-        if (kmer != null) {
+        if (actualKmer != null) {
             checkMessage |= CheckMessage.ACUTUALKMER;
-            this.kmer.setAsCopy(msg.getActualKmer());
+            this.actualKmer.setAsCopy(msg.getActualKmer());
 
         }
         if (neighberNode != null) {
@@ -89,7 +90,7 @@
         }
         if (chainVertexId != null) {
             checkMessage |= CheckMessage.ACUTUALKMER;
-            this.kmer.setAsCopy(chainVertexId);
+            this.actualKmer.setAsCopy(chainVertexId);
 
         }
         if (neighberNode != null) {
@@ -106,7 +107,7 @@
     public void reset(int kmerSize) {
         checkMessage = (byte) 0;
         kmerlength = kmerSize;
-//        kmer.reset();
+//        actualKmer.reset();
         neighberNode.reset(kmerSize);
         startVertexId.reset(kmerSize);
         averageCoverage = 0;
@@ -126,25 +127,25 @@
     }
     
     public VKmerBytesWritable getActualKmer() {
-        return kmer;
+        return actualKmer;
     }
 
     public void setActualKmer(VKmerBytesWritable actualKmer) {
         if (actualKmer != null) {
             checkMessage |= CheckMessage.ACUTUALKMER;
-            this.kmer.setAsCopy(actualKmer);
+            this.actualKmer.setAsCopy(actualKmer);
 
         }
     }
     
     public VKmerBytesWritable getCreatedVertexId() {
-        return kmer;
+        return actualKmer;
     }
 
     public void setCreatedVertexId(VKmerBytesWritable actualKmer) {
         if (actualKmer != null) {
             checkMessage |= CheckMessage.ACUTUALKMER;
-            this.kmer.setAsCopy(actualKmer);
+            this.actualKmer.setAsCopy(actualKmer);
 
         }
     }
@@ -180,7 +181,7 @@
     }
 
     public int getLengthOfChain() {
-        return kmer.getKmerLetterLength();
+        return actualKmer.getKmerLetterLength();
     }
 
     public byte getFlag() {
@@ -226,7 +227,7 @@
         if ((checkMessage & CheckMessage.SOURCE) != 0)
             sourceVertexId.write(out);
         if ((checkMessage & CheckMessage.ACUTUALKMER) != 0)
-            kmer.write(out);
+            actualKmer.write(out);
         if ((checkMessage & CheckMessage.NEIGHBER) != 0)
             neighberNode.write(out);
         if ((checkMessage & CheckMessage.NODEIDLIST) != 0)
@@ -247,7 +248,7 @@
         if ((checkMessage & CheckMessage.SOURCE) != 0)
             sourceVertexId.readFields(in);
         if ((checkMessage & CheckMessage.ACUTUALKMER) != 0)
-            kmer.readFields(in);
+            actualKmer.readFields(in);
         if ((checkMessage & CheckMessage.NEIGHBER) != 0)
             neighberNode.readFields(in);
         if ((checkMessage & CheckMessage.NODEIDLIST) != 0)
@@ -290,4 +291,16 @@
             return Float.compare(left.averageCoverage, right.averageCoverage);
         }
     }
+    
+    /**
+     * Update my coverage to be the average of this and other. Used when merging paths.
+     */
+    public void mergeCoverage(MessageWritable other) {
+        // sequence considered in the average doesn't include anything overlapping with other kmers
+        float adjustedLength = actualKmer.getKmerLetterLength() + other.actualKmer.getKmerLetterLength() - (KmerBytesWritable.getKmerLength() - 1) * 2;
+        
+        float myCount = (actualKmer.getKmerLetterLength() - KmerBytesWritable.getKmerLength() - 1) * averageCoverage;
+        float otherCount = (other.actualKmer.getKmerLetterLength() - KmerBytesWritable.getKmerLength() - 1) * other.averageCoverage;
+        averageCoverage = (myCount + otherCount) / adjustedLength;
+    }
 }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
index 245fe85..3a37794 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
@@ -6,6 +6,8 @@
 
 import edu.uci.ics.genomix.type.PositionListWritable;
 import edu.uci.ics.genomix.pregelix.type.MessageFlag;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.NodeWritable;
 import edu.uci.ics.genomix.type.VKmerBytesWritable;
 import edu.uci.ics.genomix.type.VKmerListWritable;
 
@@ -360,5 +362,4 @@
         }
     }
     
-
 }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
index c92148f..c97244a 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
@@ -29,6 +29,8 @@
     
     private Map<VKmerBytesWritable, ArrayList<MessageWritable>> receivedMsgMap = new HashMap<VKmerBytesWritable, ArrayList<MessageWritable>>();
     private ArrayList<MessageWritable> receivedMsgList = new ArrayList<MessageWritable>();
+    private Set<MessageWritable> unchangedSet = new HashSet<MessageWritable>();
+    private Set<MessageWritable> deletedSet = new HashSet<MessageWritable>();
 
     /**
      * initiate kmerSize, maxIteration
@@ -96,6 +98,48 @@
         }
     }
     
+    public void processSimilarSetToUnchangeSetAndDeletedSet(){
+        unchangedSet.clear();
+        deletedSet.clear();
+        MessageWritable topCoverageMessage = new MessageWritable();
+        MessageWritable tmpMessage = new MessageWritable();
+        Iterator<MessageWritable> it;
+        while(!receivedMsgList.isEmpty()){
+            it = receivedMsgList.iterator();
+            topCoverageMessage.set(it.next());
+            it.remove(); //delete topCoverage node
+            while(it.hasNext()){
+                tmpMessage.set(it.next());
+                //compute the similarity  
+                float fracDissimilar = topCoverageMessage.getSourceVertexId().fracDissimilar(tmpMessage.getSourceVertexId());
+                if(fracDissimilar < dissimilarThreshold){ //If similar with top node, delete this node and put it in deletedSet 
+                    //add coverage to top node
+                    topCoverageMessage.mergeCoverage(tmpMessage);
+                    deletedSet.add(tmpMessage);
+                    it.remove();
+                }
+            }
+            unchangedSet.add(topCoverageMessage);
+        }
+    }
+    
+    public void processUnchangedSet(){
+        for(MessageWritable msg : unchangedSet){
+            outFlag = MessageFlag.UNCHANGE;
+            outgoingMsg.setFlag(outFlag);
+            outgoingMsg.setAverageCoverage(msg.getAverageCoverage());
+            sendMsg(msg.getSourceVertexId(), outgoingMsg);
+        }
+    }
+    
+    public void processDeletedSet(){
+        for(MessageWritable msg : deletedSet){
+            outFlag = MessageFlag.KILL;
+            outgoingMsg.setFlag(outFlag);
+            sendMsg(msg.getSourceVertexId(), outgoingMsg);
+        }
+    }
+    
     @Override
     public void compute(Iterator<MessageWritable> msgIterator) {
         initVertex();
@@ -116,8 +160,7 @@
             /** aggregate bubble nodes and grouped by major vertex **/ 
             aggregateBubbleNodesByMajorNode(msgIterator);
             
-            Set<MessageWritable> unchangedSet = new HashSet<MessageWritable>();
-            Set<MessageWritable> deletedSet = new HashSet<MessageWritable>();
+            
             for(VKmerBytesWritable prevId : receivedMsgMap.keySet()){
                 if(receivedMsgList.size() > 1){ // filter bubble
                     /** for each startVertex, sort the node by decreasing order of coverage **/
@@ -125,38 +168,11 @@
                     Collections.sort(receivedMsgList, new MessageWritable.SortByCoverage());
                     
                     /** process similarSet, keep the unchanged set and deleted set & add coverage to unchange node **/
-                    MessageWritable topCoverageMessage = new MessageWritable();
-                    MessageWritable tmpMessage = new MessageWritable();
-                    Iterator<MessageWritable> it;
-                    while(!receivedMsgList.isEmpty()){
-                        it = receivedMsgList.iterator();
-                        topCoverageMessage.set(it.next());
-                        it.remove(); //delete topCoverage node
-                        while(it.hasNext()){
-                            tmpMessage.set(it.next());
-                            //compute the similarity  
-                            float fracDissimilar = (float) 0.02;
-                            if(fracDissimilar < dissimilarThreshold){ //If similar with top node, delete this node and put it in deletedSet 
-                                //TODO add coverage to top node
-                                deletedSet.add(tmpMessage);
-                                it.remove();
-                            }
-                        }
-                        unchangedSet.add(topCoverageMessage);
-                    }
+                    processSimilarSetToUnchangeSetAndDeletedSet();
                     
                     /** send message to the unchanged set for updating coverage & send kill message to the deleted set **/ 
-                    for(MessageWritable msg : unchangedSet){
-                        outFlag = MessageFlag.UNCHANGE;
-                        outgoingMsg.setFlag(outFlag);
-                        outgoingMsg.setAverageCoverage(msg.getAverageCoverage());
-                        sendMsg(msg.getSourceVertexId(), outgoingMsg);
-                    }
-                    for(MessageWritable msg : deletedSet){
-                        outFlag = MessageFlag.KILL;
-                        outgoingMsg.setFlag(outFlag);
-                        sendMsg(msg.getSourceVertexId(), outgoingMsg);
-                    }
+                    processUnchangedSet();
+                    processDeletedSet();
                 }
             }
         } else if (getSuperstep() == 4){
@@ -165,6 +181,7 @@
                 if(incomingMsg.getFlag() == MessageFlag.KILL){
                     broadcaseKillself();
                 } else if(incomingMsg.getFlag() == MessageFlag.UNCHANGE){
+                    /** update average coverage **/
                     getVertexValue().setAverageCoverage(incomingMsg.getAverageCoverage());
                 }
             }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/VertexUtil.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/VertexUtil.java
index 4582557..e2e7dfb 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/VertexUtil.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/VertexUtil.java
@@ -2,6 +2,7 @@
 
 import edu.uci.ics.genomix.pregelix.io.AdjacencyListWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
 import edu.uci.ics.genomix.type.VKmerBytesWritable;
 
 public class VertexUtil {
@@ -124,4 +125,5 @@
         else
             return null;
     }
+    
 }
diff --git a/genomix/genomix-pregelix/src/test/resources/only_bubbleadd.txt b/genomix/genomix-pregelix/src/test/resources/only_bubbleadd.txt
new file mode 100644
index 0000000..a4c7fc8
--- /dev/null
+++ b/genomix/genomix-pregelix/src/test/resources/only_bubbleadd.txt
@@ -0,0 +1 @@
+BubbleAddGraph.xml