--- a/src/KmerIndex.cpp
+++ b/src/KmerIndex.cpp
@@ -4,7 +4,7 @@
 #include <ctype.h>
 #include <zlib.h>
 #include <unordered_set>
-#include "kseq.h"
+#include <htslib/kseq.h>
 
 #ifndef KSEQ_INIT_READY
 #define KSEQ_INIT_READY
--- a/src/ProcessReads.cpp
+++ b/src/ProcessReads.cpp
@@ -1,6 +1,6 @@
 /*
 #include <zlib.h>
-#include "kseq.h"
+#include <htslib/kseq.h>
 #include <string>
 #include <vector>
 #include <unordered_map>
@@ -20,7 +20,7 @@
 #include <iomanip>
 
 #include "ProcessReads.h"
-#include "kseq.h"
+#include <htslib/kseq.h>
 #include "PseudoBam.h"
 #include "Fusion.hpp"
 #include "BUSData.h"
--- a/src/ProcessReads.h
+++ b/src/ProcessReads.h
@@ -2,7 +2,7 @@
 #define KALLISTO_PROCESSREADS_H
 
 #include <zlib.h>
-#include "kseq.h"
+#include <htslib/kseq.h>
 #include <string>
 #include <vector>
 #include <unordered_map>
--- a/unit_tests/test_kmerhashtable.cpp
+++ b/unit_tests/test_kmerhashtable.cpp
@@ -13,7 +13,7 @@
 #include "KmerHashTable.h"
 
 #include <zlib.h>
-#include "kseq.h"
+#include <htslib/kseq.h>
 
 #ifndef KSEQ_INIT_READY
 #define KSEQ_INIT_READY