diff --git a/src/peprocessor.cpp b/src/peprocessor.cpp
index 8ff63b9..b54ce4d 100644
--- a/src/peprocessor.cpp
+++ b/src/peprocessor.cpp
@@ -58,6 +58,12 @@ PairEndProcessor::~PairEndProcessor() {
         delete mRightReadPool;
         mRightReadPool = NULL;
     }
+    for(int t=0; t<mOptions->thread; t++){
+        delete mLeftInputLists[t];
+        delete mRightInputLists[t];
+    }
+    delete[] mLeftInputLists;
+    delete[] mRightInputLists;
 }
 
 void PairEndProcessor::initOutput() {
diff --git a/src/read.cpp b/src/read.cpp
index c155784..05a1bd1 100644
--- a/src/read.cpp
+++ b/src/read.cpp
@@ -56,7 +56,6 @@ Read* Read::reverseComplement(){
 	string seq = Sequence::reverseComplement(mSeq);
 	string qual;
 	qual.assign(mQuality->rbegin(), mQuality->rend());
-	string* strand=new string("+");
 	return new Read(mName->c_str(), seq.c_str(), "+", qual.c_str());
 }
 
diff --git a/src/readpool.cpp b/src/readpool.cpp
index 577c8f9..c5bd953 100644
--- a/src/readpool.cpp
+++ b/src/readpool.cpp
@@ -31,8 +31,15 @@ bool ReadPool::input(int tid, Read* data) {
 }
 
 void ReadPool::cleanup() {
-    //TODO: delete unused pooled Reads.
-    //But since this is only called when the program exits, the one-by-one deletion can be skipped to save time
+    for(int t=0; t<mOptions->thread; t++) {
+        while(mBufferLists[t]->canBeConsumed()) {
+            Read* r = mBufferLists[t]->consume();
+            mConsumed++;
+            delete r;
+        }
+        delete mBufferLists[t];
+    }
+    delete[] mBufferLists;
 }
 
 void ReadPool::initBufferLists() {
diff --git a/src/seprocessor.cpp b/src/seprocessor.cpp
index ccb7b11..41fc921 100644
--- a/src/seprocessor.cpp
+++ b/src/seprocessor.cpp
@@ -41,6 +41,10 @@ SingleEndProcessor::~SingleEndProcessor() {
         delete mReadPool;
         mReadPool = NULL;
     }
+    for(int t=0; t<mOptions->thread; t++){
+        delete mInputLists[t];
+    }
+    delete[] mInputLists;
 }
 
 void SingleEndProcessor::initOutput() {
diff --git a/src/singleproducersingleconsumerlist.h b/src/singleproducersingleconsumerlist.h
index dd90b4b..ee80647 100644
--- a/src/singleproducersingleconsumerlist.h
+++ b/src/singleproducersingleconsumerlist.h
@@ -83,6 +83,8 @@ class SingleProducerSingleConsumerList {
             blocks[recycled & blocksRingBufferSizeMask] = NULL;
             recycled++;
         }
+        delete[] blocks;
+        blocks = NULL;
     }
     inline size_t size() {
         return produced -  consumed;
diff --git a/src/threadconfig.cpp b/src/threadconfig.cpp
index 02ebd2a..b3f2407 100644
--- a/src/threadconfig.cpp
+++ b/src/threadconfig.cpp
@@ -41,6 +41,26 @@ void ThreadConfig::cleanup() {
         delete mRightInputList;
         mRightInputList = NULL;
     }
+    if(mPreStats1) {
+        delete mPreStats1;
+        mPreStats1 = NULL;
+    }
+    if(mPostStats1) {
+        delete mPostStats1;
+        mPostStats1 = NULL;
+    }
+    if(mPreStats2) {
+        delete mPreStats2;
+        mPreStats2 = NULL;
+    }
+    if(mPostStats2) {
+        delete mPostStats2;
+        mPostStats2 = NULL;
+    }
+    if(mFilterResult) {
+        delete mFilterResult;
+        mFilterResult = NULL;
+    }
 }
 
 
diff --git a/src/writerthread.cpp b/src/writerthread.cpp
index df6c508..f64f2ff 100644
--- a/src/writerthread.cpp
+++ b/src/writerthread.cpp
@@ -55,6 +55,11 @@ void WriterThread::input(int tid, string* data) {
 
 void WriterThread::cleanup() {
     deleteWriter();
+    for(int t=0; t<mOptions->thread; t++) {
+        delete mBufferLists[t];
+    }
+    delete[] mBufferLists;
+    mBufferLists = NULL;
 }
 
 void WriterThread::deleteWriter() {