diff --git a/Makefile b/Makefile
index 17b13b64..45169319 100644
--- a/Makefile
+++ b/Makefile
@@ -1,5 +1,5 @@
-CFLAGS=		-g -Wall -O2 -Wc++-compat #-Wextra
-CPPFLAGS=	-DHAVE_KALLOC
+CFLAGS+=		-g -Wall -O2 -Wc++-compat #-Wextra
+CPPFLAGS+=	-DHAVE_KALLOC
 INCLUDES=
 OBJS=		kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o \
 			lchain.o align.o hit.o seed.o map.o format.o pe.o esterr.o splitidx.o \
@@ -49,55 +49,55 @@ all:$(PROG)
 extra:all $(PROG_EXTRA)
 
 minimap2:main.o libminimap2.a
-		$(CC) $(CFLAGS) main.o -o $@ -L. -lminimap2 $(LIBS)
+		$(CC) $(CFLAGS) $(LDFLAGS) main.o -o $@ -L. -lminimap2 $(LIBS)
 
 minimap2-lite:example.o libminimap2.a
-		$(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS)
+		$(CC) $(CFLAGS) $(LDFLAGS) $< -o $@ -L. -lminimap2 $(LIBS)
 
 libminimap2.a:$(OBJS)
 		$(AR) -csru $@ $(OBJS)
 
 sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h ketopt.h sdust.h
-		$(CC) -D_SDUST_MAIN $(CFLAGS) $< kalloc.o -o $@ -lz
+		$(CC) -D_SDUST_MAIN $(CFLAGS) $(LDFLAGS) $< kalloc.o -o $@ -lz
 
 # SSE-specific targets on x86/x86_64
 
 ifeq ($(arm_neon),)   # if arm_neon is defined, compile this target with the default setting (i.e. no -msse2)
 ksw2_ll_sse.o:ksw2_ll_sse.c ksw2.h kalloc.h
-		$(CC) -c $(CFLAGS) -msse2 $(CPPFLAGS) $(INCLUDES) $< -o $@
+		$(CC) -c $(CFLAGS) $(LDFLAGS) -msse2 $(CPPFLAGS) $(INCLUDES) $< -o $@
 endif
 
 ksw2_extz2_sse41.o:ksw2_extz2_sse.c ksw2.h kalloc.h
-		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
+		$(CC) -c $(CFLAGS) $(LDFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
 
 ksw2_extz2_sse2.o:ksw2_extz2_sse.c ksw2.h kalloc.h
-		$(CC) -c $(CFLAGS) -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
+		$(CC) -c $(CFLAGS) $(LDFLAGS) -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
 
 ksw2_extd2_sse41.o:ksw2_extd2_sse.c ksw2.h kalloc.h
-		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
+		$(CC) -c $(CFLAGS) $(LDFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
 
 ksw2_extd2_sse2.o:ksw2_extd2_sse.c ksw2.h kalloc.h
-		$(CC) -c $(CFLAGS) -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
+		$(CC) -c $(CFLAGS) $(LDFLAGS) -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
 
 ksw2_exts2_sse41.o:ksw2_exts2_sse.c ksw2.h kalloc.h
-		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
+		$(CC) -c $(CFLAGS) $(LDFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
 
 ksw2_exts2_sse2.o:ksw2_exts2_sse.c ksw2.h kalloc.h
-		$(CC) -c $(CFLAGS) -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
+		$(CC) -c $(CFLAGS) $(LDFLAGS) -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
 
 ksw2_dispatch.o:ksw2_dispatch.c ksw2.h
-		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
+		$(CC) -c $(CFLAGS) $(LDFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
 
 # NEON-specific targets on ARM
 
 ksw2_extz2_neon.o:ksw2_extz2_sse.c ksw2.h kalloc.h
-		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
+		$(CC) -c $(CFLAGS) $(LDFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
 
 ksw2_extd2_neon.o:ksw2_extd2_sse.c ksw2.h kalloc.h
-		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
+		$(CC) -c $(CFLAGS) $(LDFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
 
 ksw2_exts2_neon.o:ksw2_exts2_sse.c ksw2.h kalloc.h
-		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
+		$(CC) -c $(CFLAGS) $(LDFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
 
 # other non-file targets