diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryDataCleanVertexInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryDataCleanVertexInputFormat.java
new file mode 100644
index 0000000..d3d52f3
--- /dev/null
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryDataCleanVertexInputFormat.java
@@ -0,0 +1,104 @@
+package edu.uci.ics.genomix.pregelix.api.io.binary;
+
+import java.io.IOException;
+import java.util.List;
+
+import org.apache.hadoop.io.Writable;
+import org.apache.hadoop.io.WritableComparable;
+import org.apache.hadoop.mapreduce.InputSplit;
+import org.apache.hadoop.mapreduce.JobContext;
+import org.apache.hadoop.mapreduce.RecordReader;
+import org.apache.hadoop.mapreduce.TaskAttemptContext;
+import org.apache.hadoop.mapreduce.lib.input.SequenceFileInputFormat;
+
+import edu.uci.ics.pregelix.api.io.VertexInputFormat;
+import edu.uci.ics.pregelix.api.io.VertexReader;
+import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.type.PositionWritable;
+
+public class BinaryDataCleanVertexInputFormat<I extends WritableComparable<?>, V extends Writable, E extends Writable, M extends Writable>
+        extends VertexInputFormat<I, V, E, M> {
+
+    /** Uses the SequenceFileInputFormat to do everything */
+    @SuppressWarnings("rawtypes")
+    protected SequenceFileInputFormat binaryInputFormat = new SequenceFileInputFormat();
+
+    /**
+     * Abstract class to be implemented by the user based on their specific
+     * vertex input. Easiest to ignore the key value separator and only use key
+     * instead.
+     * 
+     * @param <I>
+     *            Vertex index value
+     * @param <V>
+     *            Vertex value
+     * @param <E>
+     *            Edge value
+     */
+    public static abstract class BinaryDataCleanVertexReader<I extends WritableComparable<?>, V extends Writable, E extends Writable, M extends Writable>
+            implements VertexReader<I, V, E, M> {
+        /** Internal line record reader */
+        private final RecordReader<PositionWritable, ValueStateWritable> lineRecordReader;
+        /** Context passed to initialize */
+        private TaskAttemptContext context;
+
+        /**
+         * Initialize with the LineRecordReader.
+         * 
+         * @param recordReader
+         *            Line record reader from SequenceFileInputFormat
+         */
+        public BinaryDataCleanVertexReader(RecordReader<PositionWritable, ValueStateWritable> recordReader) {
+            this.lineRecordReader = recordReader;
+        }
+
+        @Override
+        public void initialize(InputSplit inputSplit, TaskAttemptContext context) throws IOException,
+                InterruptedException {
+            lineRecordReader.initialize(inputSplit, context);
+            this.context = context;
+        }
+
+        @Override
+        public void close() throws IOException {
+            lineRecordReader.close();
+        }
+
+        @Override
+        public float getProgress() throws IOException, InterruptedException {
+            return lineRecordReader.getProgress();
+        }
+
+        /**
+         * Get the line record reader.
+         * 
+         * @return Record reader to be used for reading.
+         */
+        protected RecordReader<PositionWritable, ValueStateWritable> getRecordReader() {
+            return lineRecordReader;
+        }
+
+        /**
+         * Get the context.
+         * 
+         * @return Context passed to initialize.
+         */
+        protected TaskAttemptContext getContext() {
+            return context;
+        }
+    }
+
+    @SuppressWarnings("unchecked")
+    @Override
+    public List<InputSplit> getSplits(JobContext context, int numWorkers) throws IOException, InterruptedException {
+        // Ignore the hint of numWorkers here since we are using SequenceFileInputFormat
+        // to do this for us
+        return binaryInputFormat.getSplits(context);
+    }
+
+    @Override
+    public VertexReader<I, V, E, M> createVertexReader(InputSplit split, TaskAttemptContext context) throws IOException {
+        return null;
+    }
+
+}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java
index 94b0c51..e135085 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java
@@ -9,9 +9,9 @@
 import org.kohsuke.args4j.CmdLineParser;
 import org.kohsuke.args4j.Option;
 
-import edu.uci.ics.genomix.pregelix.operator.LogAlgorithmForPathMergeVertex;
-import edu.uci.ics.genomix.pregelix.operator.NaiveAlgorithmForPathMergeVertex;
-import edu.uci.ics.genomix.pregelix.operator.P3ForPathMergeVertex;
+import edu.uci.ics.genomix.pregelix.operator.pathmerge.LogAlgorithmForPathMergeVertex;
+import edu.uci.ics.genomix.pregelix.operator.pathmerge.NaiveAlgorithmForPathMergeVertex;
+import edu.uci.ics.genomix.pregelix.operator.pathmerge.P3ForPathMergeVertex;
 import edu.uci.ics.pregelix.api.job.PregelixJob;
 import edu.uci.ics.pregelix.core.base.IDriver.Plan;
 import edu.uci.ics.pregelix.core.driver.Driver;
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/DataCleanInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/DataCleanInputFormat.java
new file mode 100644
index 0000000..140a703
--- /dev/null
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/DataCleanInputFormat.java
@@ -0,0 +1,74 @@
+package edu.uci.ics.genomix.pregelix.format;
+
+import java.io.IOException;
+
+import org.apache.hadoop.io.NullWritable;
+import org.apache.hadoop.mapreduce.InputSplit;
+import org.apache.hadoop.mapreduce.RecordReader;
+import org.apache.hadoop.mapreduce.TaskAttemptContext;
+
+import edu.uci.ics.genomix.type.PositionWritable;
+import edu.uci.ics.pregelix.api.graph.Vertex;
+import edu.uci.ics.pregelix.api.io.VertexReader;
+import edu.uci.ics.pregelix.api.util.BspUtils;
+import edu.uci.ics.genomix.pregelix.io.MessageWritable;
+import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryDataCleanVertexInputFormat;
+import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryDataCleanVertexInputFormat.BinaryDataCleanVertexReader;
+
+public class DataCleanInputFormat extends
+    BinaryDataCleanVertexInputFormat<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> {
+    /**
+     * Format INPUT
+     */
+    @SuppressWarnings("unchecked")
+    @Override
+    public VertexReader<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> createVertexReader(
+            InputSplit split, TaskAttemptContext context) throws IOException {
+        return new BinaryDataCleanLoadGraphReader(binaryInputFormat.createRecordReader(split, context));
+    }
+}
+
+@SuppressWarnings("rawtypes")
+class BinaryDataCleanLoadGraphReader extends
+    BinaryDataCleanVertexReader<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> {
+    private Vertex vertex;
+    private PositionWritable vertexId = new PositionWritable();
+    private ValueStateWritable vertexValue = new ValueStateWritable();
+
+    public BinaryDataCleanLoadGraphReader(RecordReader<PositionWritable, ValueStateWritable> recordReader) {
+        super(recordReader);
+    }
+
+    @Override
+    public boolean nextVertex() throws IOException, InterruptedException {
+        return getRecordReader().nextKeyValue();
+    }
+
+    @SuppressWarnings("unchecked")
+    @Override
+    public Vertex<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> getCurrentVertex()
+            throws IOException, InterruptedException {
+        if (vertex == null)
+            vertex = (Vertex) BspUtils.createVertex(getContext().getConfiguration());
+
+        vertex.getMsgList().clear();
+        vertex.getEdges().clear();
+
+        vertex.reset();
+        if (getRecordReader() != null) {
+            /**
+             * set the src vertex id
+             */
+            vertexId.set(getRecordReader().getCurrentKey());
+            vertex.setVertexId(vertexId);
+            /**
+             * set the vertex value
+             */
+            vertexValue.set(getRecordReader().getCurrentValue());
+            vertex.setVertexValue(vertexValue);
+        }
+
+        return vertex;
+    }
+}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/DataCleanOutputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/DataCleanOutputFormat.java
new file mode 100644
index 0000000..40abd3e
--- /dev/null
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/DataCleanOutputFormat.java
@@ -0,0 +1,41 @@
+package edu.uci.ics.genomix.pregelix.format;
+
+import java.io.IOException;
+
+import org.apache.hadoop.io.NullWritable;
+import org.apache.hadoop.mapreduce.RecordWriter;
+import org.apache.hadoop.mapreduce.TaskAttemptContext;
+
+import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryVertexOutputFormat;
+import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.type.PositionWritable;
+import edu.uci.ics.pregelix.api.graph.Vertex;
+import edu.uci.ics.pregelix.api.io.VertexWriter;
+
+public class DataCleanOutputFormat extends
+        BinaryVertexOutputFormat<PositionWritable, ValueStateWritable, NullWritable> {
+
+    @Override
+    public VertexWriter<PositionWritable, ValueStateWritable, NullWritable> createVertexWriter(
+            TaskAttemptContext context) throws IOException, InterruptedException {
+        @SuppressWarnings("unchecked")
+        RecordWriter<PositionWritable, ValueStateWritable> recordWriter = binaryOutputFormat.getRecordWriter(context);
+        return new BinaryLoadGraphVertexWriter(recordWriter);
+    }
+
+    /**
+     * Simple VertexWriter that supports {@link BinaryLoadGraphVertex}
+     */
+    public static class BinaryLoadGraphVertexWriter extends
+            BinaryVertexWriter<PositionWritable, ValueStateWritable, NullWritable> {
+        public BinaryLoadGraphVertexWriter(RecordWriter<PositionWritable, ValueStateWritable> lineRecordWriter) {
+            super(lineRecordWriter);
+        }
+
+        @Override
+        public void writeVertex(Vertex<PositionWritable, ValueStateWritable, NullWritable, ?> vertex)
+                throws IOException, InterruptedException {
+            getRecordWriter().write(vertex.getVertexId(), vertex.getVertexValue());
+        }
+    }
+}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/ValueStateWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/ValueStateWritable.java
index 985c2ac..7895da4 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/ValueStateWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/ValueStateWritable.java
@@ -29,7 +29,7 @@
                 reverseForwardList, reverseReverseList,
                 state, mergeChain);
     }
-
+    
     public void set(PositionListWritable forwardForwardList, PositionListWritable forwardReverseList,
             PositionListWritable reverseForwardList, PositionListWritable reverseReverseList, 
             byte state, KmerBytesWritable mergeChain) {
@@ -41,6 +41,11 @@
         this.mergeChain.set(mergeChain);
     }
     
+    public void set(ValueStateWritable value) {
+        set(value.getFFList(),value.getFRList(),value.getRFList(),value.getRRList(),value.getState(),
+                value.getMergeChain());
+    }
+    
     public PositionListWritable getFFList() {
         return outgoingList.getForwardList();
     }
@@ -78,7 +83,7 @@
     }
 
     public void setIncomingList(AdjacencyListWritable incomingList) {
-        this.incomingList = incomingList;
+        this.incomingList.set(incomingList);
     }
 
     public AdjacencyListWritable getOutgoingList() {
@@ -86,7 +91,7 @@
     }
 
     public void setOutgoingList(AdjacencyListWritable outgoingList) {
-        this.outgoingList = outgoingList;
+        this.outgoingList.set(outgoingList);
     }
 
     public byte getState() {
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/LogAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
similarity index 99%
rename from genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/LogAlgorithmForPathMergeVertex.java
rename to genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
index c3bb663..84c7f52 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/LogAlgorithmForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
@@ -1,4 +1,4 @@
-package edu.uci.ics.genomix.pregelix.operator;
+package edu.uci.ics.genomix.pregelix.operator.pathmerge;
 
 import java.util.Iterator;
 
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/NaiveAlgorithmForPathMergeVertex.java
similarity index 99%
rename from genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveAlgorithmForPathMergeVertex.java
rename to genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/NaiveAlgorithmForPathMergeVertex.java
index 4fcc09e..722206a 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveAlgorithmForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/NaiveAlgorithmForPathMergeVertex.java
@@ -1,4 +1,4 @@
-package edu.uci.ics.genomix.pregelix.operator;
+package edu.uci.ics.genomix.pregelix.operator.pathmerge;
 
 import java.util.Iterator;
 import org.apache.hadoop.io.NullWritable;
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/P3ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java
similarity index 99%
rename from genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/P3ForPathMergeVertex.java
rename to genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java
index 8a03aa7..5ba5f31 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/P3ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java
@@ -1,4 +1,4 @@
-package edu.uci.ics.genomix.pregelix.operator;
+package edu.uci.ics.genomix.pregelix.operator.pathmerge;
 
 import java.util.Iterator;
 import org.apache.hadoop.io.NullWritable;
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/BridgeRemoveVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/BridgeRemoveVertex.java
new file mode 100644
index 0000000..bdabaa4
--- /dev/null
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/BridgeRemoveVertex.java
@@ -0,0 +1,89 @@
+package edu.uci.ics.genomix.pregelix.operator.tipremove;
+
+import java.util.Iterator;
+import org.apache.hadoop.io.NullWritable;
+
+import edu.uci.ics.genomix.type.PositionWritable;
+import edu.uci.ics.pregelix.api.graph.Vertex;
+import edu.uci.ics.pregelix.api.job.PregelixJob;
+import edu.uci.ics.genomix.pregelix.client.Client;
+import edu.uci.ics.genomix.pregelix.format.DataCleanInputFormat;
+import edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat;
+import edu.uci.ics.genomix.pregelix.io.MessageWritable;
+import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+
+/*
+ * vertexId: BytesWritable
+ * vertexValue: ByteWritable
+ * edgeValue: NullWritable
+ * message: MessageWritable
+ * 
+ * DNA:
+ * A: 00
+ * C: 01
+ * G: 10
+ * T: 11
+ * 
+ * succeed node
+ *  A 00000001 1
+ *  G 00000010 2
+ *  C 00000100 4
+ *  T 00001000 8
+ * precursor node
+ *  A 00010000 16
+ *  G 00100000 32
+ *  C 01000000 64
+ *  T 10000000 128
+ *  
+ * For example, ONE LINE in input file: 00,01,10    0001,0010,
+ * That means that vertexId is ACG, its succeed node is A and its precursor node is C.
+ * The succeed node and precursor node will be stored in vertexValue and we don't use edgeValue.
+ * The details about message are in edu.uci.ics.pregelix.example.io.MessageWritable. 
+ */
+/**
+ * Naive Algorithm for path merge graph
+ */
+public class BridgeRemoveVertex extends
+        Vertex<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> {
+    public static final String KMER_SIZE = "BridgeRemoveVertex.kmerSize";
+    public static final String ITERATIONS = "BridgeRemoveVertex.iteration";
+    public static int kmerSize = -1;
+    private int maxIteration = -1;
+
+    private MessageWritable incomingMsg = new MessageWritable();
+    private MessageWritable outgoingMsg = new 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);
+        outgoingMsg.reset();
+    }
+
+    @Override
+    public void compute(Iterator<MessageWritable> msgIterator) {
+        initVertex();
+        if (getSuperstep() == 1) {
+          
+        } 
+    }
+
+    public static void main(String[] args) throws Exception {
+        PregelixJob job = new PregelixJob(BridgeRemoveVertex.class.getSimpleName());
+        job.setVertexClass(BridgeRemoveVertex.class);
+        /**
+         * BinaryInput and BinaryOutput
+         */
+        job.setVertexInputFormatClass(DataCleanInputFormat.class);
+        job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
+        job.setDynamicVertexValueSize(true);
+        job.setOutputKeyClass(PositionWritable.class);
+        job.setOutputValueClass(ValueStateWritable.class);
+        Client.run(args, job);
+    }
+}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/BubbleMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/BubbleMergeVertex.java
new file mode 100644
index 0000000..f33bcd4
--- /dev/null
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/BubbleMergeVertex.java
@@ -0,0 +1,89 @@
+package edu.uci.ics.genomix.pregelix.operator.tipremove;
+
+import java.util.Iterator;
+import org.apache.hadoop.io.NullWritable;
+
+import edu.uci.ics.genomix.type.PositionWritable;
+import edu.uci.ics.pregelix.api.graph.Vertex;
+import edu.uci.ics.pregelix.api.job.PregelixJob;
+import edu.uci.ics.genomix.pregelix.client.Client;
+import edu.uci.ics.genomix.pregelix.format.DataCleanInputFormat;
+import edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat;
+import edu.uci.ics.genomix.pregelix.io.MessageWritable;
+import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+
+/*
+ * vertexId: BytesWritable
+ * vertexValue: ByteWritable
+ * edgeValue: NullWritable
+ * message: MessageWritable
+ * 
+ * DNA:
+ * A: 00
+ * C: 01
+ * G: 10
+ * T: 11
+ * 
+ * succeed node
+ *  A 00000001 1
+ *  G 00000010 2
+ *  C 00000100 4
+ *  T 00001000 8
+ * precursor node
+ *  A 00010000 16
+ *  G 00100000 32
+ *  C 01000000 64
+ *  T 10000000 128
+ *  
+ * For example, ONE LINE in input file: 00,01,10    0001,0010,
+ * That means that vertexId is ACG, its succeed node is A and its precursor node is C.
+ * The succeed node and precursor node will be stored in vertexValue and we don't use edgeValue.
+ * The details about message are in edu.uci.ics.pregelix.example.io.MessageWritable. 
+ */
+/**
+ * Naive Algorithm for path merge graph
+ */
+public class BubbleMergeVertex extends
+        Vertex<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> {
+    public static final String KMER_SIZE = "BubbleMergeVertex.kmerSize";
+    public static final String ITERATIONS = "BubbleMergeVertex.iteration";
+    public static int kmerSize = -1;
+    private int maxIteration = -1;
+
+    private MessageWritable incomingMsg = new MessageWritable();
+    private MessageWritable outgoingMsg = new 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);
+        outgoingMsg.reset();
+    }
+
+    @Override
+    public void compute(Iterator<MessageWritable> msgIterator) {
+        initVertex();
+        if (getSuperstep() == 1) {
+          
+        } 
+    }
+
+    public static void main(String[] args) throws Exception {
+        PregelixJob job = new PregelixJob(BubbleMergeVertex.class.getSimpleName());
+        job.setVertexClass(BubbleMergeVertex.class);
+        /**
+         * BinaryInput and BinaryOutput
+         */
+        job.setVertexInputFormatClass(DataCleanInputFormat.class);
+        job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
+        job.setDynamicVertexValueSize(true);
+        job.setOutputKeyClass(PositionWritable.class);
+        job.setOutputValueClass(ValueStateWritable.class);
+        Client.run(args, job);
+    }
+}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
new file mode 100644
index 0000000..7e184d1
--- /dev/null
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
@@ -0,0 +1,84 @@
+package edu.uci.ics.genomix.pregelix.operator.tipremove;
+
+import java.util.Iterator;
+import org.apache.hadoop.io.NullWritable;
+
+import edu.uci.ics.genomix.type.PositionWritable;
+import edu.uci.ics.pregelix.api.graph.Vertex;
+import edu.uci.ics.pregelix.api.job.PregelixJob;
+import edu.uci.ics.genomix.pregelix.client.Client;
+import edu.uci.ics.genomix.pregelix.format.DataCleanInputFormat;
+import edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat;
+import edu.uci.ics.genomix.pregelix.io.MessageWritable;
+import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+
+/*
+ * vertexId: BytesWritable
+ * vertexValue: ByteWritable
+ * edgeValue: NullWritable
+ * message: MessageWritable
+ * 
+ * DNA:
+ * A: 00
+ * C: 01
+ * G: 10
+ * T: 11
+ * 
+ * succeed node
+ *  A 00000001 1
+ *  G 00000010 2
+ *  C 00000100 4
+ *  T 00001000 8
+ * precursor node
+ *  A 00010000 16
+ *  G 00100000 32
+ *  C 01000000 64
+ *  T 10000000 128
+ *  
+ * For example, ONE LINE in input file: 00,01,10    0001,0010,
+ * That means that vertexId is ACG, its succeed node is A and its precursor node is C.
+ * The succeed node and precursor node will be stored in vertexValue and we don't use edgeValue.
+ * The details about message are in edu.uci.ics.pregelix.example.io.MessageWritable. 
+ */
+/**
+ *  Remove tip or single node when l > constant
+ */
+public class TipRemoveVertex extends
+        Vertex<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> {
+    public static final String KMER_SIZE = "TipRemoveVertex.kmerSize";
+    public static final String LENGTH = "TipRemoveVertex.length";
+    public static int kmerSize = -1;
+    private int length = -1;
+
+    /**
+     * initiate kmerSize, length
+     */
+    public void initVertex() {
+        if (kmerSize == -1)
+            kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
+        if(length == -1)
+            length = getContext().getConfiguration().getInt(LENGTH, kmerSize + 5);
+    }
+
+    @Override
+    public void compute(Iterator<MessageWritable> msgIterator) {
+        initVertex(); //getVertexValue().getLengthOfMergeChain() < length
+        if(getSuperstep() == 1){
+            
+        }
+    }
+
+    public static void main(String[] args) throws Exception {
+        PregelixJob job = new PregelixJob(TipRemoveVertex.class.getSimpleName());
+        job.setVertexClass(TipRemoveVertex.class);
+        /**
+         * BinaryInput and BinaryOutput
+         */
+        job.setVertexInputFormatClass(DataCleanInputFormat.class);
+        job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
+        job.setDynamicVertexValueSize(true);
+        job.setOutputKeyClass(PositionWritable.class);
+        job.setOutputValueClass(ValueStateWritable.class);
+        Client.run(args, job);
+    }
+}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/ConvertNodeToIdValue.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/ConvertNodeToIdValue.java
index b81491b..452f72d 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/ConvertNodeToIdValue.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/ConvertNodeToIdValue.java
@@ -13,7 +13,6 @@
 
 import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
 import edu.uci.ics.genomix.pregelix.type.State;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
 import edu.uci.ics.genomix.type.NodeWritable;
 import edu.uci.ics.genomix.type.PositionWritable;
 
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 cdc97c1..16b2794 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
@@ -9,9 +9,9 @@
 import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeInputFormat;
 import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
-import edu.uci.ics.genomix.pregelix.operator.LogAlgorithmForPathMergeVertex;
-import edu.uci.ics.genomix.pregelix.operator.NaiveAlgorithmForPathMergeVertex;
-import edu.uci.ics.genomix.pregelix.operator.P3ForPathMergeVertex;
+import edu.uci.ics.genomix.pregelix.operator.pathmerge.LogAlgorithmForPathMergeVertex;
+import edu.uci.ics.genomix.pregelix.operator.pathmerge.NaiveAlgorithmForPathMergeVertex;
+import edu.uci.ics.genomix.pregelix.operator.pathmerge.P3ForPathMergeVertex;
 import edu.uci.ics.genomix.type.PositionWritable;
 import edu.uci.ics.pregelix.api.job.PregelixJob;