diff --git a/genomix/genomix-pregelix/graph/BridgePath b/genomix/genomix-pregelix/graph/BridgePath
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diff --git a/genomix/genomix-pregelix/graph/mergeTest/BridgePath b/genomix/genomix-pregelix/graph/mergeTest/BridgePath
deleted file mode 100644
index 0717611..0000000
--- a/genomix/genomix-pregelix/graph/mergeTest/BridgePath
+++ /dev/null
@@ -1,2 +0,0 @@
-TTTCCACTCCGTG
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\ No newline at end of file
diff --git a/genomix/genomix-pregelix/graph/mergeTest/CyclePath b/genomix/genomix-pregelix/graph/mergeTest/CyclePath
deleted file mode 100644
index 04080f4..0000000
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diff --git a/genomix/genomix-pregelix/graph/mergeTest/LongPath b/genomix/genomix-pregelix/graph/mergeTest/LongPath
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diff --git a/genomix/genomix-pregelix/graph/mergeTest/Path b/genomix/genomix-pregelix/graph/mergeTest/Path
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diff --git a/genomix/genomix-pregelix/graph/mergeTest/SimplePath b/genomix/genomix-pregelix/graph/mergeTest/SimplePath
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-AAGACAGCAC
-GCGGCAAGAA
diff --git a/genomix/genomix-pregelix/graph/mergeTest/SinglePath b/genomix/genomix-pregelix/graph/mergeTest/SinglePath
deleted file mode 100644
index 56ef5f8..0000000
--- a/genomix/genomix-pregelix/graph/mergeTest/SinglePath
+++ /dev/null
@@ -1 +0,0 @@
-AGACAACAGT
diff --git a/genomix/genomix-pregelix/graph/mergeTest/ThreeKmer b/genomix/genomix-pregelix/graph/mergeTest/ThreeKmer
deleted file mode 100644
index ec004fa..0000000
--- a/genomix/genomix-pregelix/graph/mergeTest/ThreeKmer
+++ /dev/null
@@ -1 +0,0 @@
-ACTCGGT
diff --git a/genomix/genomix-pregelix/graph/mergeTest/TreePath b/genomix/genomix-pregelix/graph/mergeTest/TreePath
deleted file mode 100644
index f3c13ce..0000000
--- a/genomix/genomix-pregelix/graph/mergeTest/TreePath
+++ /dev/null
@@ -1,3 +0,0 @@
-GGCCTGGCTATCCC
-GGCCTCAGTAACTAAAC
-GGCCTCAGTACGCCCGG
\ No newline at end of file
diff --git a/genomix/genomix-pregelix/graph/mergeTest/TwoKmer b/genomix/genomix-pregelix/graph/mergeTest/TwoKmer
deleted file mode 100644
index 8c2a74b..0000000
--- a/genomix/genomix-pregelix/graph/mergeTest/TwoKmer
+++ /dev/null
@@ -1 +0,0 @@
-ACACTG
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 cd2425b..c686d0c 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
@@ -32,6 +32,8 @@
     private boolean updateMsg = false;
     private VKmerBytesWritable startVertexId;
     private VKmerListWritable pathList;
+    private boolean srcFlip = false;
+    private boolean destFlip = false;
     
     private byte checkMessage;
 
@@ -264,6 +266,22 @@
         }
     }
 
+    public boolean isSrcFlip() {
+        return srcFlip;
+    }
+
+    public void setSrcFlip(boolean srcFlip) {
+        this.srcFlip = srcFlip;
+    }
+
+    public boolean isDestFlip() {
+        return destFlip;
+    }
+
+    public void setDestFlip(boolean destFlip) {
+        this.destFlip = destFlip;
+    }
+
     @Override
     public void write(DataOutput out) throws IOException {
         out.writeInt(kmerlength);
@@ -284,6 +302,8 @@
         out.writeBoolean(isFlip);
         out.writeByte(flag); 
         out.writeBoolean(updateMsg);
+        out.writeBoolean(srcFlip);
+        out.writeBoolean(destFlip);
     }
 
     @Override
@@ -307,6 +327,8 @@
         isFlip = in.readBoolean();
         flag = in.readByte();
         updateMsg = in.readBoolean();
+        srcFlip = in.readBoolean();
+        destFlip = in.readBoolean();
     }
 
     @Override
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/BFSTraverseVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/BFSTraverseVertex.java
index f3abaed..ee42dee 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/BFSTraverseVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/BFSTraverseVertex.java
@@ -6,11 +6,18 @@
 import java.util.List;
 import java.util.Map;
 
+import edu.uci.ics.genomix.pregelix.client.Client;
+import edu.uci.ics.genomix.pregelix.format.GraphCleanInputFormat;
+import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
 import edu.uci.ics.genomix.pregelix.operator.pathmerge.MapReduceVertex;
+import edu.uci.ics.genomix.type.PositionListWritable;
+import edu.uci.ics.genomix.type.PositionWritable;
 import edu.uci.ics.genomix.type.VKmerBytesWritable;
 import edu.uci.ics.genomix.type.VKmerListWritable;
+import edu.uci.ics.pregelix.api.job.PregelixJob;
 
 public class BFSTraverseVertex extends
     MapReduceVertex {
@@ -63,11 +70,11 @@
         if (maxIteration < 0)
             maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 1000000);
         if(incomingMsg == null)
-            incomingMsg = new MessageWritable(kmerSize);
+            incomingMsg = new MessageWritable();
         if(outgoingMsg == null)
-            outgoingMsg = new MessageWritable(kmerSize);
+            outgoingMsg = new MessageWritable();
         else
-            outgoingMsg.reset(kmerSize);
+            outgoingMsg.reset();
         if(reverseKmer == null)
             reverseKmer = new VKmerBytesWritable();
         if(kmerList == null)
@@ -82,6 +89,8 @@
         if(destVertexId == null)
             destVertexId = new VKmerBytesWritable(kmerSize);
         isFakeVertex = ((byte)getVertexValue().getState() & State.FAKEFLAG_MASK) > 0 ? true : false;
+        if(tmpKmer == null)
+            tmpKmer = new VKmerBytesWritable();
     }
     
     public void aggregateMsgAndGroupedByReadIdInReachedNode(Iterator<MessageWritable> msgIterator){
@@ -124,6 +133,7 @@
     }
     
     public void initialBroadcaseBFSTraverse(){
+        outgoingMsg.reset();
         outgoingMsg.setSourceVertexId(getVertexId());
         outgoingMsg.setSeekedVertexId(incomingMsg.getSeekedVertexId());
         outgoingMsg.getPathList().append(getVertexId());
@@ -135,6 +145,7 @@
     }
     
     public void broadcastBFSTraverse(){
+        outgoingMsg.reset();
         outgoingMsg.setSourceVertexId(incomingMsg.getSourceVertexId());
         outgoingMsg.setSeekedVertexId(incomingMsg.getSeekedVertexId());
         outgoingMsg.getPathList().append(getVertexId());
@@ -153,12 +164,19 @@
             voteToHalt();
         }
         else if(getSuperstep() == 2){
-            kmerList.append(new VKmerBytesWritable("Kmer1"));
-            kmerList.append(new VKmerBytesWritable("Kmer2"));
+            tmpKmer.setByRead(kmerSize, "AAT".getBytes(), 0);
+            kmerList.append(tmpKmer);
+            tmpKmer.setByRead(kmerSize, "CTA".getBytes(), 0);
+            kmerList.append(tmpKmer);
             /** initiate two nodes -- srcNode and destNode **/
             srcNode.setAsCopy(kmerList.getPosition(0));
             destNode.setAsCopy(kmerList.getPosition(1));
             // outgoingMsg.setNodeIdList(); set as common readId
+            PositionWritable nodeId = new PositionWritable();
+            nodeId.set((byte) 0, 1, 0);
+            PositionListWritable nodeIdList = new PositionListWritable();
+            nodeIdList.append(nodeId);
+            outgoingMsg.setNodeIdList(nodeIdList);
             outgoingMsg.setSeekedVertexId(destNode);
             sendMsg(srcNode, outgoingMsg);
             outgoingMsg.setSeekedVertexId(srcNode);
@@ -203,4 +221,17 @@
         
     }
     
+    public static void main(String[] args) throws Exception {
+        PregelixJob job = new PregelixJob(BFSTraverseVertex.class.getSimpleName());
+        job.setVertexClass(BFSTraverseVertex.class);
+        /**
+         * BinaryInput and BinaryOutput
+         */
+        job.setVertexInputFormatClass(GraphCleanInputFormat.class);
+        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
+        job.setDynamicVertexValueSize(true);
+        job.setOutputKeyClass(VKmerBytesWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
+        Client.run(args, job);
+    }
 }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/NaiveBFSTraverseVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/NaiveBFSTraverseVertex.java
new file mode 100644
index 0000000..d5b8301
--- /dev/null
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/NaiveBFSTraverseVertex.java
@@ -0,0 +1,189 @@
+package edu.uci.ics.genomix.pregelix.operator.scaffolding;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+import edu.uci.ics.genomix.pregelix.client.Client;
+import edu.uci.ics.genomix.pregelix.format.GraphCleanInputFormat;
+import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
+import edu.uci.ics.genomix.pregelix.io.MessageWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
+import edu.uci.ics.genomix.pregelix.operator.pathmerge.MapReduceVertex;
+import edu.uci.ics.genomix.pregelix.type.MessageFlag;
+import edu.uci.ics.genomix.type.PositionListWritable;
+import edu.uci.ics.genomix.type.PositionWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerListWritable;
+import edu.uci.ics.pregelix.api.job.PregelixJob;
+
+public class NaiveBFSTraverseVertex extends
+    MapReduceVertex {
+    
+    protected VKmerBytesWritable srcNode = new VKmerBytesWritable();
+    protected VKmerBytesWritable destNode = new VKmerBytesWritable();
+    Map<Long, List<MessageWritable>> receivedMsg = new HashMap<Long, List<MessageWritable>>();
+
+    /**
+     * initiate kmerSize, maxIteration
+     */
+    public void initVertex() {
+        if (kmerSize == -1)
+            kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
+        if (maxIteration < 0)
+            maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 1000000);
+        if(incomingMsg == null)
+            incomingMsg = new MessageWritable();
+        if(outgoingMsg == null)
+            outgoingMsg = new MessageWritable();
+        else
+            outgoingMsg.reset();
+        if(reverseKmer == null)
+            reverseKmer = new VKmerBytesWritable();
+        if(kmerList == null)
+            kmerList = new VKmerListWritable();
+        else
+            kmerList.reset();
+        if(fakeVertex == null){
+            fakeVertex = new VKmerBytesWritable();
+            String random = generaterRandomString(kmerSize + 1);
+            fakeVertex.setByRead(kmerSize + 1, random.getBytes(), 0); 
+        }
+        if(destVertexId == null)
+            destVertexId = new VKmerBytesWritable(kmerSize);
+        if(tmpKmer == null)
+            tmpKmer = new VKmerBytesWritable();
+    }
+    
+    public void initialBroadcaseBFSTraverse(){
+        outgoingMsg.reset();
+        outgoingMsg.setSourceVertexId(getVertexId());
+        outgoingMsg.setSeekedVertexId(incomingMsg.getSeekedVertexId());
+        outgoingMsg.setSrcFlip(incomingMsg.isSrcFlip());
+        outgoingMsg.setDestFlip(incomingMsg.isDestFlip());
+        kmerList.append(getVertexId());
+        outgoingMsg.setPathList(kmerList);
+        outgoingMsg.setNodeIdList(incomingMsg.getNodeIdList()); //only one readId
+        if(incomingMsg.isSrcFlip())
+            sendSettledMsgToAllPreviousNodes(getVertexValue());
+        else
+            sendSettledMsgToAllNextNodes(getVertexValue());
+    }
+    
+    public void broadcaseBFSTraverse(){
+        outgoingMsg.reset();
+        outgoingMsg.setSourceVertexId(incomingMsg.getSourceVertexId());
+        outgoingMsg.setSeekedVertexId(incomingMsg.getSeekedVertexId());
+        outgoingMsg.setSrcFlip(incomingMsg.isSrcFlip());
+        outgoingMsg.setDestFlip(incomingMsg.isDestFlip());
+        kmerList.setCopy(incomingMsg.getPathList());
+        kmerList.append(getVertexId());
+        outgoingMsg.setPathList(kmerList);
+        outgoingMsg.setNodeIdList(incomingMsg.getNodeIdList()); //only one readId
+        byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
+        byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+        switch(neighborToMeDir){
+            case MessageFlag.DIR_FF:
+            case MessageFlag.DIR_FR:
+                sendSettledMsgToAllPreviousNodes(getVertexValue());
+                break;
+            case MessageFlag.DIR_RF:
+            case MessageFlag.DIR_RR:
+                sendSettledMsgToAllNextNodes(getVertexValue());
+                break;
+        }
+    }
+    
+    public boolean isValidDestination(){
+        byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
+        byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+        if(incomingMsg.isDestFlip())
+            return neighborToMeDir == MessageFlag.DIR_RF || neighborToMeDir == MessageFlag.DIR_RR;
+        else
+            return neighborToMeDir == MessageFlag.DIR_FF || neighborToMeDir == MessageFlag.DIR_FR;
+    }
+  
+    public void initiateSrcAndDestNode(VKmerListWritable pairKmerList, ArrayList<Boolean> flagList, 
+            PositionListWritable nodeIdList){
+        initiateSrcAndDestNode(pairKmerList, flagList.get(0), flagList.get(1), nodeIdList);
+    }
+    
+    public void initiateSrcAndDestNode(VKmerListWritable pairKmerList, boolean srcFlip, boolean destFlip, 
+            PositionListWritable nodeIdList){
+        srcNode.setAsCopy(pairKmerList.getPosition(0));
+        destNode.setAsCopy(pairKmerList.getPosition(1));
+        outgoingMsg.setNodeIdList(nodeIdList);
+        outgoingMsg.setSeekedVertexId(destNode);
+        outgoingMsg.setSrcFlip(srcFlip);
+        outgoingMsg.setDestFlip(destFlip);
+    }
+    
+    @Override
+    public void compute(Iterator<MessageWritable> msgIterator) {
+        initVertex();
+        if(getSuperstep() == 1){
+            addFakeVertex();
+            voteToHalt();
+        }
+        else if(getSuperstep() == 2){
+            tmpKmer.setByRead(kmerSize, "AAT".getBytes(), 0);
+            kmerList.append(tmpKmer);
+            tmpKmer.setByRead(kmerSize, "AGA".getBytes(), 0);
+            kmerList.append(tmpKmer);
+            // outgoingMsg.setNodeIdList(); set as common readId
+            PositionWritable nodeId = new PositionWritable();
+            nodeId.set((byte) 0, 1, 0);
+            PositionListWritable nodeIdList = new PositionListWritable();
+            nodeIdList.append(nodeId);
+            /** initiate two nodes -- srcNode and destNode **/
+            initiateSrcAndDestNode(kmerList, true, false, nodeIdList);
+            sendMsg(srcNode, outgoingMsg);
+            
+            deleteVertex(getVertexId());
+        } else if(getSuperstep() == 3){
+            while(msgIterator.hasNext()){
+                incomingMsg = msgIterator.next();
+                /** begin to BFS **/
+                initialBroadcaseBFSTraverse();
+            }
+            voteToHalt();
+        } else if(getSuperstep() > 3){
+            while(msgIterator.hasNext()){
+                incomingMsg = msgIterator.next();
+                /** check if find destination **/
+                if(incomingMsg.getSeekedVertexId().equals(getVertexId())){
+                    if(isValidDestination()){
+                        kmerList.setCopy(incomingMsg.getPathList());
+                        kmerList.append(getVertexId());
+                        //TODO do some process after finding a path
+                    }
+                    else{
+                        //keep BFS
+                        broadcaseBFSTraverse();
+                    }
+                } else {
+                    //keep BFS
+                    broadcaseBFSTraverse();
+                }
+            }
+            voteToHalt();
+        }
+        
+    }
+    
+    public static void main(String[] args) throws Exception {
+        PregelixJob job = new PregelixJob(NaiveBFSTraverseVertex.class.getSimpleName());
+        job.setVertexClass(NaiveBFSTraverseVertex.class);
+        /**
+         * BinaryInput and BinaryOutput
+         */
+        job.setVertexInputFormatClass(GraphCleanInputFormat.class);
+        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
+        job.setDynamicVertexValueSize(true);
+        job.setOutputKeyClass(VKmerBytesWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
+        Client.run(args, job);
+    }
+}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/ScaffoldingVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/ScaffoldingVertex.java
index 782ed70..bf55cb1 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/ScaffoldingVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/ScaffoldingVertex.java
@@ -1,19 +1,60 @@
 package edu.uci.ics.genomix.pregelix.operator.scaffolding;
 
+import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.Map;
 
 import edu.uci.ics.genomix.pregelix.io.HashMapWritable;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
-import edu.uci.ics.genomix.pregelix.operator.pathmerge.MapReduceVertex;
+import edu.uci.ics.genomix.type.PositionListWritable;
+import edu.uci.ics.genomix.type.PositionWritable;
 import edu.uci.ics.genomix.type.VKmerBytesWritable;
 import edu.uci.ics.genomix.type.VKmerListWritable;
 
 public class ScaffoldingVertex extends 
-    MapReduceVertex{
+    NaiveBFSTraverseVertex{
 
-    public static Map<Long, VKmerListWritable> scaffoldingMap = new HashMap<Long, VKmerListWritable>();
+    public class KmerListAndFlagList{
+        private ArrayList<Boolean> flagList;
+        private VKmerListWritable kmerList;
+        
+        public KmerListAndFlagList(){
+            flagList = new ArrayList<Boolean>();
+            kmerList = new VKmerListWritable();
+        }
+        
+        public void set(KmerListAndFlagList kmerAndflag){
+            flagList.clear();
+            kmerList.reset();
+            flagList.addAll(kmerAndflag.getFlagList());
+            kmerList.appendList(kmerAndflag.getKmerList());
+        }
+        
+        public int size(){
+            return flagList.size();
+        }
+        
+        public ArrayList<Boolean> getFlagList() {
+            return flagList;
+        }
+
+        public void setFlagList(ArrayList<Boolean> flagList) {
+            this.flagList = flagList;
+        }
+
+        public VKmerListWritable getKmerList() {
+            return kmerList;
+        }
+
+        public void setKmerList(VKmerListWritable kmerList) {
+            this.kmerList = kmerList;
+        }
+        
+    }
+    private ArrayList<Boolean> flagList = new ArrayList<Boolean>();
+    private KmerListAndFlagList kmerListAndflagList = new KmerListAndFlagList();
+    public static Map<Long, KmerListAndFlagList> scaffoldingMap = new HashMap<Long, KmerListAndFlagList>();
     
     private HashMapWritable<VKmerBytesWritable, VKmerListWritable> traverseMap = new HashMapWritable<VKmerBytesWritable, VKmerListWritable>();
     
@@ -39,34 +80,74 @@
             kmerList = new VKmerListWritable();
     }
     
+    public void addStartReadsToScaffoldingMap(){
+        boolean isflip = false;
+        for(PositionWritable pos : getVertexValue().getStartReads()){
+            long readId = pos.getReadId();
+            if(scaffoldingMap.containsKey(readId)){
+                kmerList.setCopy(scaffoldingMap.get(readId).getKmerList());
+                kmerList.append(getVertexId());
+                flagList.clear();
+                flagList.addAll(scaffoldingMap.get(readId).getFlagList());
+                flagList.add(isflip);
+            } else{
+                kmerList.reset();
+                kmerList.append(getVertexId());
+                flagList.clear();
+                flagList.add(isflip);
+            }
+            kmerListAndflagList.setKmerList(kmerList);
+            kmerListAndflagList.setFlagList(flagList);
+            scaffoldingMap.put(readId, kmerListAndflagList);
+        }
+    }
+    
+    public void addEndReadsToScaffoldingMap(){
+        boolean isflip = true;
+        for(PositionWritable pos : getVertexValue().getEndReads()){
+            long readId = pos.getReadId();
+            if(scaffoldingMap.containsKey(readId)){
+                kmerList.setCopy(scaffoldingMap.get(readId).getKmerList());
+                kmerList.append(getVertexId());
+                flagList.clear();
+                flagList.addAll(scaffoldingMap.get(readId).getFlagList());
+                flagList.add(isflip);
+            } else{
+                kmerList.reset();
+                kmerList.append(getVertexId());
+                flagList.clear();
+                flagList.add(isflip);
+            }
+            kmerListAndflagList.setKmerList(kmerList);
+            kmerListAndflagList.setFlagList(flagList);
+            scaffoldingMap.put(readId, kmerListAndflagList);
+        }
+    }
+    
     @Override
     public void compute(Iterator<MessageWritable> msgIterator) {
         initVertex();
         if(getSuperstep() == 1){
             /** add a fake vertex **/
             addFakeVertex();
-            /** grouped by 5' readId **/ //TODO
-            long mainReadId = getVertexValue().getStartReads().getPosition(0).getReadId();
-            if(mainReadId != 0){ //empty or not
-                if(scaffoldingMap.containsKey(mainReadId)){
-                    kmerList.setCopy(scaffoldingMap.get(mainReadId));
-                    kmerList.append(getVertexId());
-                } else{
-                    kmerList.reset();
-                    kmerList.append(getVertexId());
-                }
-                scaffoldingMap.put(mainReadId, kmerList);
-            }
+            /** grouped by 5' readId **/
+            addStartReadsToScaffoldingMap();
+            addEndReadsToScaffoldingMap();
+            
             voteToHalt();
         } else if(getSuperstep() == 2){
             /** process scaffoldingMap **/
             for(Long readId : scaffoldingMap.keySet()){
-                kmerList.setCopy(scaffoldingMap.get(readId));
-                if(kmerList.getCountOfPosition() == 2){
-                    outgoingMsg.setSeekedVertexId(kmerList.getPosition(1));
-                    sendMsg(kmerList.getPosition(0), outgoingMsg);
-                    outgoingMsg.setSeekedVertexId(kmerList.getPosition(0));
-                    sendMsg(kmerList.getPosition(1), outgoingMsg);
+                ////////////
+                PositionWritable nodeId = new PositionWritable();
+                nodeId.set((byte) 0, 1, 0);
+                PositionListWritable nodeIdList = new PositionListWritable();
+                nodeIdList.append(nodeId);
+                ////////////
+                kmerListAndflagList.set(scaffoldingMap.get(readId));
+                if(kmerListAndflagList.size() == 2){
+                    initiateSrcAndDestNode(kmerListAndflagList.kmerList, kmerListAndflagList.flagList, nodeIdList);
+                    sendMsg(srcNode, outgoingMsg);
                 }
             }
             deleteVertex(getVertexId());
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/splitrepeat/SimpleSplitRepeatVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/splitrepeat/SimpleSplitRepeatVertex.java
new file mode 100644
index 0000000..3ab95b9
--- /dev/null
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/splitrepeat/SimpleSplitRepeatVertex.java
@@ -0,0 +1,29 @@
+package edu.uci.ics.genomix.pregelix.operator.splitrepeat;
+
+import edu.uci.ics.genomix.pregelix.io.MessageWritable;
+import edu.uci.ics.genomix.pregelix.operator.pathmerge.BasicGraphCleanVertex;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
+
+public class SimpleSplitRepeatVertex extends 
+    BasicGraphCleanVertex{
+    
+    /**
+     * initiate kmerSize, maxIteration
+     */
+    public void initVertex() {
+        if (kmerSize == -1)
+            kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
+        if (maxIteration < 0)
+            maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 1000000);
+        if(incomingMsg == null)
+            incomingMsg = new MessageWritable(kmerSize);
+        if(outgoingMsg == null)
+            outgoingMsg = new MessageWritable(kmerSize);
+        else
+            outgoingMsg.reset(kmerSize);
+        if(destVertexId == null)
+            destVertexId = new VKmerBytesWritable(kmerSize);
+        if(tmpKmer == null)
+            tmpKmer = new VKmerBytesWritable();
+    }
+}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/testcase/GenerateTestInput.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/testcase/GenerateTestInput.java
index f30512c..f73a5de 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/testcase/GenerateTestInput.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/testcase/GenerateTestInput.java
@@ -9,24 +9,38 @@
     /**
      * Simple Path
      */
-    public static String simplePath(int k, int length, int numLines) {
-        RandomString rs = new RandomString(k, length);
+    public static String simplePath(int kmerSize, int readLength, int numLines) {
+        RandomString rs = new RandomString(kmerSize, readLength);
         String output = "";
         for (int i = 0; i < numLines; i++)
             output += rs.nextString(0) + "\r\n";
         return output;
+        
     }
 
     /**
+     * Bridge Path
+     */
+    public static String bridgePath(int kmerSize, int headLength, int bridgeLength, int readLength) {
+        RandomString rs = new RandomString(kmerSize, readLength);
+        String s1 = rs.nextString(0);
+        rs.setLength(headLength + bridgeLength);
+        int startBridge = kmerSize + headLength;
+        rs.addString(s1.substring(0, startBridge));
+        String s2 = rs.nextString(startBridge) + s1.substring(bridgeLength + startBridge - kmerSize);
+        return s1 + "\r\n" + s2;
+    }
+    
+    /**
      * Tree Path
      */
-    public static String treePath(int k, int x, int y, int z) {
-        RandomString rs = new RandomString(k, x + y + k - 1);
+    public static String treePath(int kmerSize, int x, int y, int z) {
+        RandomString rs = new RandomString(kmerSize, x + y + kmerSize - 1);
         String s1 = rs.nextString(0);
-        rs.setLength(x + y + z + k - 1);
+        rs.setLength(x + y + z + kmerSize - 1);
         rs.addString(s1.substring(0, x));
         String s2 = rs.nextString(x);
-        rs.setLength(x + y + z + k - 1);
+        rs.setLength(x + y + z + kmerSize - 1);
         rs.addString(s2.substring(0, x + y));
         String s3 = rs.nextString(x + y);
         return s1 + "\r\n" + s2 + "\r\n" + s3;
@@ -35,46 +49,74 @@
     /**
      * Cycle Path
      */
-    public static String cyclePath(int k, int length) {
-        RandomString rs = new RandomString(k, length);
+    public static String cyclePath(int kmerSize, int length) {
+        RandomString rs = new RandomString(kmerSize, length);
         String s1 = rs.nextString(0);
-        String s2 = s1 + s1.substring(1, k + 1);
+        String s2 = s1 + s1.substring(1, kmerSize + 1);
         return s2;
     }
-
-    /**
-     * Bridge Path
-     */
-    public static String bridgePath(int k, int x) {
-        RandomString rs = new RandomString(k, x + k + 2 + k - 1);
-        String s1 = rs.nextString(0);
-        rs.setLength(x + k + 2);
-        rs.addString(s1.substring(0, k + 2));
-        String s2 = rs.nextString(k + 2) + s1.substring(x + k + 2, x + k + 2 + k - 1);
-        return s1 + "\r\n" + s2;
-    }
-
-    public static void main(String[] args) {
-        // TODO Auto-generated method stub
+    
+    public static void generateSimplePath(String destDir, int kmerSize, int readLength, int numLines){
         OutputStreamWriter writer;
         try {
-            writer = new OutputStreamWriter(new FileOutputStream("graph/7/SinglePath"));
-            writer.write(simplePath(7, 10, 1));
-            writer.close();
-            writer = new OutputStreamWriter(new FileOutputStream("graph/7/SimplePath"));
-            writer.write(simplePath(7, 10, 3));
-            writer.close();
-            writer = new OutputStreamWriter(new FileOutputStream("graph/7/TreePath"));
-            writer.write(treePath(7, 7, 7, 7));
-            writer.close();
-            writer = new OutputStreamWriter(new FileOutputStream("graph/7/CyclePath"));
-            writer.write(cyclePath(7, 10));
-            writer.close();
-            writer = new OutputStreamWriter(new FileOutputStream("graph/7/BridgePath"));
-            writer.write(bridgePath(7, 2));
+            writer = new OutputStreamWriter(new FileOutputStream(destDir));
+            writer.write(simplePath(kmerSize, readLength, numLines));
             writer.close();
         } catch (IOException e) {
             e.printStackTrace();
         }
     }
+    
+    public static void generateBridgePath(String destDir, int kmerSize, int headLength, int bridgeLength, int readLength){
+        OutputStreamWriter writer;
+        try {
+            writer = new OutputStreamWriter(new FileOutputStream(destDir));
+            writer.write(bridgePath(kmerSize, headLength, bridgeLength, readLength));
+            writer.close();
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+    }
+    
+    public static void generateTreePath(String destDir, int kmerSize, int x, int y, int z){
+        OutputStreamWriter writer;
+        try {
+            writer = new OutputStreamWriter(new FileOutputStream(destDir));
+            writer.write(treePath(kmerSize, x, y, z));
+            writer.close();
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+    }
+    
+    public static void generateCyclePath(String destDir, int kmerSize, int cycleLength){
+        OutputStreamWriter writer;
+        try {
+            writer = new OutputStreamWriter(new FileOutputStream(destDir));
+            writer.write(cyclePath(kmerSize, cycleLength));
+            writer.close();
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+    }
+    
+    public static void main(String[] args) {
+        int kmerSize = 3; 
+        /** SimplePath **/
+        int readLength = 9;
+        int numLines = 3;
+        generateSimplePath("graph/SimplePath", kmerSize, readLength, numLines);
+        /** BridgePath **/
+        int headLength = 2;
+        int bridgeLength = 4; 
+        generateBridgePath("graph/BridgePath", kmerSize, headLength, bridgeLength, readLength);
+        /** TreePath **/
+        int x = 5;
+        int y = 5;
+        int z = 5;
+        generateTreePath("graph/TreePath", kmerSize, x, y, z);
+        /** CyclePath **/
+        int cycleLength = 8;
+        generateCyclePath("graph/CyclePath", kmerSize, cycleLength);
+    }
 }
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
index 98219d7..be6885b 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
@@ -17,6 +17,7 @@
 import edu.uci.ics.genomix.pregelix.operator.pathmerge.MapReduceVertex;
 import edu.uci.ics.genomix.pregelix.operator.pathmerge.P4ForPathMergeVertex;
 import edu.uci.ics.genomix.pregelix.operator.removelowcoverage.RemoveLowCoverageVertex;
+import edu.uci.ics.genomix.pregelix.operator.scaffolding.NaiveBFSTraverseVertex;
 import edu.uci.ics.genomix.pregelix.operator.scaffolding.ScaffoldingVertex;
 import edu.uci.ics.genomix.pregelix.operator.splitrepeat.SplitRepeatVertex;
 import edu.uci.ics.genomix.pregelix.operator.tipremove.TipAddVertex;
@@ -249,6 +250,23 @@
                 + "BubbleMergeGraph.xml");
     }
     
+    private static void generateNaiveBFSTraverseGraphJob(String jobName, String outputPath) throws IOException {
+        PregelixJob job = new PregelixJob(jobName);
+        job.setVertexClass(NaiveBFSTraverseVertex.class);
+        job.setVertexInputFormatClass(InitialGraphCleanInputFormat.class);
+        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
+        job.setDynamicVertexValueSize(true);
+        job.setOutputKeyClass(VKmerBytesWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
+        job.getConfiguration().setInt(ScaffoldingVertex.KMER_SIZE, 3);
+        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
+    }
+
+    private static void genNaiveBFSTraverseGraph() throws IOException {
+        generateNaiveBFSTraverseGraphJob("NaiveBFSTraversegGraph", outputBase
+                + "NaiveBFSTraverseGraph.xml");
+    }
+    
     private static void generateScaffoldingGraphJob(String jobName, String outputPath) throws IOException {
         PregelixJob job = new PregelixJob(jobName);
         job.setVertexClass(ScaffoldingVertex.class);
@@ -278,6 +296,7 @@
         genBubbleAddGraph();
         genBubbleMergeGraph();
         genSplitRepeatGraph();
+        genNaiveBFSTraverseGraph();
         genScaffoldingGraph();
     }
 
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BFSTraverseSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BFSTraverseSmallTestSuite.java
new file mode 100644
index 0000000..41b0d8b
--- /dev/null
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BFSTraverseSmallTestSuite.java
@@ -0,0 +1,201 @@
+/*
+ * Copyright 2009-2010 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package edu.uci.ics.genomix.pregelix.JobRun;
+
+import java.io.BufferedReader;
+import java.io.DataOutputStream;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.logging.Logger;
+
+import junit.framework.Test;
+import junit.framework.TestResult;
+import junit.framework.TestSuite;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.hdfs.MiniDFSCluster;
+import org.apache.hadoop.mapred.JobConf;
+
+import edu.uci.ics.pregelix.core.jobgen.clusterconfig.ClusterConfig;
+import edu.uci.ics.pregelix.core.util.PregelixHyracksIntegrationUtil;
+
+@SuppressWarnings("deprecation")
+public class BFSTraverseSmallTestSuite extends TestSuite {
+    private static final Logger LOGGER = Logger.getLogger(BFSTraverseSmallTestSuite.class.getName());
+    //P4ForMergeGraph/bin/read
+    public static final String PreFix = "data/PathMergeTestSet"; 
+    public static final String[] TestDir = { PreFix + File.separator
+    + "4"};
+    private static final String ACTUAL_RESULT_DIR = "data/actual/BTSTraverse";
+    private static final String PATH_TO_HADOOP_CONF = "src/test/resources/hadoop/conf";
+    private static final String PATH_TO_CLUSTER_STORE = "src/test/resources/cluster/stores.properties";
+    private static final String PATH_TO_CLUSTER_PROPERTIES = "src/test/resources/cluster/cluster.properties";
+    private static final String PATH_TO_JOBS = "src/test/resources/jobs/";
+    private static final String PATH_TO_ONLY = "src/test/resources/only_BFSTraverse.txt";
+
+    public static final String HDFS_INPUTPATH = "/PathTestSet";
+
+    private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR + File.separator + "conf.xml";
+    private MiniDFSCluster dfsCluster;
+
+    private JobConf conf = new JobConf();
+    private int numberOfNC = 1;
+
+    public void setUp() throws Exception {
+        ClusterConfig.setStorePath(PATH_TO_CLUSTER_STORE);
+        ClusterConfig.setClusterPropertiesPath(PATH_TO_CLUSTER_PROPERTIES);
+        cleanupStores();
+        PregelixHyracksIntegrationUtil.init();
+        LOGGER.info("Hyracks mini-cluster started");
+        FileUtils.forceMkdir(new File(ACTUAL_RESULT_DIR));
+        FileUtils.cleanDirectory(new File(ACTUAL_RESULT_DIR));
+        startHDFS();
+    }
+
+    private void startHDFS() throws IOException {
+        conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/core-site.xml"));
+        conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/mapred-site.xml"));
+        conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/hdfs-site.xml"));
+        FileSystem lfs = FileSystem.getLocal(new Configuration());
+        lfs.delete(new Path("build"), true);
+        System.setProperty("hadoop.log.dir", "logs");
+        dfsCluster = new MiniDFSCluster(conf, numberOfNC, true, null);
+        FileSystem dfs = FileSystem.get(conf);
+
+        for (String testDir : TestDir) {
+            File src = new File(testDir);
+            Path dest = new Path(HDFS_INPUTPATH + File.separator + src.getName());
+            dfs.mkdirs(dest);
+            //src.listFiles()
+            //src.listFiles((FilenameFilter)(new WildcardFileFilter("part*")))
+            for (File f : src.listFiles()) {
+                dfs.copyFromLocalFile(new Path(f.getAbsolutePath()), dest);
+            }
+        }
+
+        DataOutputStream confOutput = new DataOutputStream(new FileOutputStream(new File(HADOOP_CONF_PATH)));
+        conf.writeXml(confOutput);
+        confOutput.flush();
+        confOutput.close();
+    }
+
+    private void cleanupStores() throws IOException {
+        FileUtils.forceMkdir(new File("teststore"));
+        FileUtils.forceMkdir(new File("build"));
+        FileUtils.cleanDirectory(new File("teststore"));
+        FileUtils.cleanDirectory(new File("build"));
+    }
+
+    /**
+     * cleanup hdfs cluster
+     */
+    private void cleanupHDFS() throws Exception {
+        dfsCluster.shutdown();
+    }
+
+    public void tearDown() throws Exception {
+        PregelixHyracksIntegrationUtil.deinit();
+        LOGGER.info("Hyracks mini-cluster shut down");
+        cleanupHDFS();
+    }
+
+    public static Test suite() throws Exception {
+        List<String> onlys = getFileList(PATH_TO_ONLY);
+        File testData = new File(PATH_TO_JOBS);
+        File[] queries = testData.listFiles();
+        BFSTraverseSmallTestSuite testSuite = new BFSTraverseSmallTestSuite();
+        testSuite.setUp();
+        boolean onlyEnabled = false;
+        FileSystem dfs = FileSystem.get(testSuite.conf);
+
+        if (onlys.size() > 0) {
+            onlyEnabled = true;
+        }
+
+        for (File qFile : queries) {
+            if (qFile.isFile()) {
+                if (onlyEnabled && !isInList(onlys, qFile.getName())) {
+                    continue;
+                } else {
+                    for (String testPathStr : TestDir) {
+                        File testDir = new File(testPathStr);
+                        String resultFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName())
+                                + File.separator + "bin" + File.separator + testDir.getName();
+                        String textFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName())
+                                + File.separator + "txt" + File.separator + testDir.getName();
+                        String graphvizFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName())
+                                + File.separator + "graphviz" + File.separator + testDir.getName();
+                        testSuite.addTest(new BasicSmallTestCase(HADOOP_CONF_PATH, qFile.getName(), qFile
+                                .getAbsolutePath().toString(), dfs,
+                                HDFS_INPUTPATH + File.separator + testDir.getName(), resultFileName, textFileName, graphvizFileName));
+                    }
+                }
+            }
+        }
+        return testSuite;
+    }
+
+    /**
+     * Runs the tests and collects their result in a TestResult.
+     */
+    @Override
+    public void run(TestResult result) {
+        try {
+            int testCount = countTestCases();
+            for (int i = 0; i < testCount; i++) {
+                // cleanupStores();
+                Test each = this.testAt(i);
+                if (result.shouldStop())
+                    break;
+                runTest(each, result);
+            }
+            tearDown();
+        } catch (Exception e) {
+            throw new IllegalStateException(e);
+        }
+    }
+
+    protected static List<String> getFileList(String ignorePath) throws FileNotFoundException, IOException {
+        BufferedReader reader = new BufferedReader(new FileReader(ignorePath));
+        String s = null;
+        List<String> ignores = new ArrayList<String>();
+        while ((s = reader.readLine()) != null) {
+            ignores.add(s);
+        }
+        reader.close();
+        return ignores;
+    }
+
+    private static String jobExtToResExt(String fname) {
+        int dot = fname.lastIndexOf('.');
+        return fname.substring(0, dot);
+    }
+
+    private static boolean isInList(List<String> onlys, String name) {
+        for (String only : onlys)
+            if (name.indexOf(only) >= 0)
+                return true;
+        return false;
+    }
+
+}
diff --git a/genomix/genomix-pregelix/src/test/resources/jobs/NaiveBFSTraverseGraph.xml b/genomix/genomix-pregelix/src/test/resources/jobs/NaiveBFSTraverseGraph.xml
new file mode 100644
index 0000000..a412b2b
--- /dev/null
+++ b/genomix/genomix-pregelix/src/test/resources/jobs/NaiveBFSTraverseGraph.xml
@@ -0,0 +1,142 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?><configuration>
+<property><name>mapred.tasktracker.dns.nameserver</name><value>default</value></property>
+<property><name>mapred.queue.default.acl-administer-jobs</name><value>*</value></property>
+<property><name>mapred.skip.map.auto.incr.proc.count</name><value>true</value></property>
+<property><name>mapred.jobtracker.instrumentation</name><value>org.apache.hadoop.mapred.JobTrackerMetricsInst</value></property>
+<property><name>mapred.skip.reduce.auto.incr.proc.count</name><value>true</value></property>
+<property><name>fs.hsftp.impl</name><value>org.apache.hadoop.hdfs.HsftpFileSystem</value></property>
+<property><name>mapred.submit.replication</name><value>10</value></property>
+<property><name>ipc.server.tcpnodelay</name><value>false</value></property>
+<property><name>fs.checkpoint.dir</name><value>${hadoop.tmp.dir}/dfs/namesecondary</value></property>
+<property><name>mapred.output.compression.type</name><value>RECORD</value></property>
+<property><name>mapred.job.shuffle.merge.percent</name><value>0.66</value></property>
+<property><name>mapred.child.java.opts</name><value>-Xmx200m</value></property>
+<property><name>mapred.queue.default.acl-submit-job</name><value>*</value></property>
+<property><name>keep.failed.task.files</name><value>false</value></property>
+<property><name>mapred.jobtracker.job.history.block.size</name><value>3145728</value></property>
+<property><name>mapred.output.value.class</name><value>edu.uci.ics.genomix.pregelix.io.VertexValueWritable</value></property>
+<property><name>io.bytes.per.checksum</name><value>512</value></property>
+<property><name>mapred.task.tracker.report.address</name><value>127.0.0.1:0</value></property>
+<property><name>hadoop.util.hash.type</name><value>murmur</value></property>
+<property><name>fs.hdfs.impl</name><value>org.apache.hadoop.hdfs.DistributedFileSystem</value></property>
+<property><name>fs.ramfs.impl</name><value>org.apache.hadoop.fs.InMemoryFileSystem</value></property>
+<property><name>mapred.jobtracker.restart.recover</name><value>false</value></property>
+<property><name>fs.hftp.impl</name><value>org.apache.hadoop.hdfs.HftpFileSystem</value></property>
+<property><name>fs.checkpoint.period</name><value>3600</value></property>
+<property><name>mapred.child.tmp</name><value>./tmp</value></property>
+<property><name>mapred.local.dir.minspacekill</name><value>0</value></property>
+<property><name>map.sort.class</name><value>org.apache.hadoop.util.QuickSort</value></property>
+<property><name>hadoop.logfile.count</name><value>10</value></property>
+<property><name>ipc.client.connection.maxidletime</name><value>10000</value></property>
+<property><name>io.map.index.skip</name><value>0</value></property>
+<property><name>mapred.tasktracker.expiry.interval</name><value>600000</value></property>
+<property><name>mapred.output.compress</name><value>false</value></property>
+<property><name>io.seqfile.lazydecompress</name><value>true</value></property>
+<property><name>mapred.reduce.parallel.copies</name><value>5</value></property>
+<property><name>fs.checkpoint.size</name><value>67108864</value></property>
+<property><name>mapred.job.reduce.input.buffer.percent</name><value>0.0</value></property>
+<property><name>mapred.job.name</name><value>NaiveBFSTraversegGraph</value></property>
+<property><name>local.cache.size</name><value>10737418240</value></property>
+<property><name>fs.s3n.impl</name><value>org.apache.hadoop.fs.s3native.NativeS3FileSystem</value></property>
+<property><name>mapred.userlog.limit.kb</name><value>0</value></property>
+<property><name>fs.file.impl</name><value>org.apache.hadoop.fs.LocalFileSystem</value></property>
+<property><name>mapred.task.tracker.http.address</name><value>0.0.0.0:50060</value></property>
+<property><name>mapred.task.timeout</name><value>600000</value></property>
+<property><name>fs.kfs.impl</name><value>org.apache.hadoop.fs.kfs.KosmosFileSystem</value></property>
+<property><name>mapred.max.tracker.blacklists</name><value>4</value></property>
+<property><name>fs.s3.buffer.dir</name><value>${hadoop.tmp.dir}/s3</value></property>
+<property><name>mapred.job.tracker.persist.jobstatus.dir</name><value>/jobtracker/jobsInfo</value></property>
+<property><name>ipc.client.kill.max</name><value>10</value></property>
+<property><name>mapred.tasktracker.instrumentation</name><value>org.apache.hadoop.mapred.TaskTrackerMetricsInst</value></property>
+<property><name>mapred.reduce.tasks.speculative.execution</name><value>true</value></property>
+<property><name>io.sort.record.percent</name><value>0.05</value></property>
+<property><name>hadoop.security.authorization</name><value>false</value></property>
+<property><name>mapred.max.tracker.failures</name><value>4</value></property>
+<property><name>mapred.jobtracker.taskScheduler</name><value>org.apache.hadoop.mapred.JobQueueTaskScheduler</value></property>
+<property><name>mapred.tasktracker.dns.interface</name><value>default</value></property>
+<property><name>mapred.map.tasks</name><value>2</value></property>
+<property><name>mapred.job.tracker.persist.jobstatus.hours</name><value>0</value></property>
+<property><name>fs.s3.sleepTimeSeconds</name><value>10</value></property>
+<property><name>fs.default.name</name><value>file:///</value></property>
+<property><name>mapred.output.key.class</name><value>edu.uci.ics.genomix.type.VKmerBytesWritable</value></property>
+<property><name>tasktracker.http.threads</name><value>40</value></property>
+<property><name>mapred.tasktracker.taskmemorymanager.monitoring-interval</name><value>5000</value></property>
+<property><name>hadoop.rpc.socket.factory.class.default</name><value>org.apache.hadoop.net.StandardSocketFactory</value></property>
+<property><name>mapred.reduce.tasks</name><value>1</value></property>
+<property><name>topology.node.switch.mapping.impl</name><value>org.apache.hadoop.net.ScriptBasedMapping</value></property>
+<property><name>pregelix.vertexClass</name><value>edu.uci.ics.genomix.pregelix.operator.scaffolding.NaiveBFSTraverseVertex</value></property>
+<property><name>mapred.skip.reduce.max.skip.groups</name><value>0</value></property>
+<property><name>io.file.buffer.size</name><value>4096</value></property>
+<property><name>mapred.jobtracker.maxtasks.per.job</name><value>-1</value></property>
+<property><name>mapred.tasktracker.indexcache.mb</name><value>10</value></property>
+<property><name>mapred.tasktracker.map.tasks.maximum</name><value>2</value></property>
+<property><name>fs.har.impl.disable.cache</name><value>true</value></property>
+<property><name>mapred.task.profile.maps</name><value>0-2</value></property>
+<property><name>hadoop.native.lib</name><value>true</value></property>
+<property><name>fs.s3.block.size</name><value>67108864</value></property>
+<property><name>mapred.job.reuse.jvm.num.tasks</name><value>1</value></property>
+<property><name>mapred.job.tracker.http.address</name><value>0.0.0.0:50030</value></property>
+<property><name>mapred.tasktracker.reduce.tasks.maximum</name><value>2</value></property>
+<property><name>io.compression.codecs</name><value>org.apache.hadoop.io.compress.DefaultCodec,org.apache.hadoop.io.compress.GzipCodec,org.apache.hadoop.io.compress.BZip2Codec</value></property>
+<property><name>mapred.job.shuffle.input.buffer.percent</name><value>0.70</value></property>
+<property><name>io.seqfile.compress.blocksize</name><value>1000000</value></property>
+<property><name>mapred.queue.names</name><value>default</value></property>
+<property><name>fs.har.impl</name><value>org.apache.hadoop.fs.HarFileSystem</value></property>
+<property><name>io.mapfile.bloom.error.rate</name><value>0.005</value></property>
+<property><name>mapred.job.tracker</name><value>local</value></property>
+<property><name>BasicGraphCleanVertex.kmerSize</name><value>3</value></property>
+<property><name>io.skip.checksum.errors</name><value>false</value></property>
+<property><name>mapred.reduce.max.attempts</name><value>4</value></property>
+<property><name>fs.s3.maxRetries</name><value>4</value></property>
+<property><name>ipc.server.listen.queue.size</name><value>128</value></property>
+<property><name>fs.trash.interval</name><value>0</value></property>
+<property><name>mapred.local.dir.minspacestart</name><value>0</value></property>
+<property><name>fs.s3.impl</name><value>org.apache.hadoop.fs.s3.S3FileSystem</value></property>
+<property><name>io.seqfile.sorter.recordlimit</name><value>1000000</value></property>
+<property><name>io.mapfile.bloom.size</name><value>1048576</value></property>
+<property><name>io.sort.mb</name><value>100</value></property>
+<property><name>mapred.local.dir</name><value>${hadoop.tmp.dir}/mapred/local</value></property>
+<property><name>io.sort.factor</name><value>10</value></property>
+<property><name>mapred.task.profile</name><value>false</value></property>
+<property><name>job.end.retry.interval</name><value>30000</value></property>
+<property><name>mapred.tasktracker.procfsbasedprocesstree.sleeptime-before-sigkill</name><value>5000</value></property>
+<property><name>mapred.jobtracker.completeuserjobs.maximum</name><value>100</value></property>
+<property><name>mapred.task.profile.reduces</name><value>0-2</value></property>
+<property><name>webinterface.private.actions</name><value>false</value></property>
+<property><name>hadoop.tmp.dir</name><value>/tmp/hadoop-${user.name}</value></property>
+<property><name>mapred.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
+<property><name>mapred.skip.attempts.to.start.skipping</name><value>2</value></property>
+<property><name>mapred.temp.dir</name><value>${hadoop.tmp.dir}/mapred/temp</value></property>
+<property><name>mapred.merge.recordsBeforeProgress</name><value>10000</value></property>
+<property><name>mapred.map.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
+<property><name>mapred.compress.map.output</name><value>false</value></property>
+<property><name>io.sort.spill.percent</name><value>0.80</value></property>
+<property><name>fs.checkpoint.edits.dir</name><value>${fs.checkpoint.dir}</value></property>
+<property><name>mapred.userlog.retain.hours</name><value>24</value></property>
+<property><name>mapred.system.dir</name><value>${hadoop.tmp.dir}/mapred/system</value></property>
+<property><name>mapred.line.input.format.linespermap</name><value>1</value></property>
+<property><name>job.end.retry.attempts</name><value>0</value></property>
+<property><name>ipc.client.idlethreshold</name><value>4000</value></property>
+<property><name>pregelix.vertexOutputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat</value></property>
+<property><name>mapred.reduce.copy.backoff</name><value>300</value></property>
+<property><name>mapred.map.tasks.speculative.execution</name><value>true</value></property>
+<property><name>mapred.inmem.merge.threshold</name><value>1000</value></property>
+<property><name>hadoop.logfile.size</name><value>10000000</value></property>
+<property><name>pregelix.vertexInputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.InitialGraphCleanInputFormat</value></property>
+<property><name>mapred.job.queue.name</name><value>default</value></property>
+<property><name>mapred.job.tracker.persist.jobstatus.active</name><value>false</value></property>
+<property><name>pregelix.incStateLength</name><value>true</value></property>
+<property><name>mapred.reduce.slowstart.completed.maps</name><value>0.05</value></property>
+<property><name>topology.script.number.args</name><value>100</value></property>
+<property><name>mapred.skip.map.max.skip.records</name><value>0</value></property>
+<property><name>fs.ftp.impl</name><value>org.apache.hadoop.fs.ftp.FTPFileSystem</value></property>
+<property><name>mapred.task.cache.levels</name><value>2</value></property>
+<property><name>mapred.job.tracker.handler.count</name><value>10</value></property>
+<property><name>io.serializations</name><value>org.apache.hadoop.io.serializer.WritableSerialization</value></property>
+<property><name>ipc.client.connect.max.retries</name><value>10</value></property>
+<property><name>mapred.min.split.size</name><value>0</value></property>
+<property><name>mapred.map.max.attempts</name><value>4</value></property>
+<property><name>jobclient.output.filter</name><value>FAILED</value></property>
+<property><name>ipc.client.tcpnodelay</name><value>false</value></property>
+<property><name>mapred.acls.enabled</name><value>false</value></property>
+</configuration>
\ No newline at end of file
diff --git a/genomix/genomix-pregelix/src/test/resources/only_BFSTraverse.txt b/genomix/genomix-pregelix/src/test/resources/only_BFSTraverse.txt
new file mode 100644
index 0000000..92aae74
--- /dev/null
+++ b/genomix/genomix-pregelix/src/test/resources/only_BFSTraverse.txt
@@ -0,0 +1 @@
+NaiveBFSTraverseGraph.xml