diff -ur bowtie-1.2.3.org/Makefile bowtie-1.2.3/Makefile
--- bowtie-1.2.3.org/Makefile	2019-09-26 12:14:35.498557693 +0900
+++ bowtie-1.2.3/Makefile	2019-09-26 12:15:17.262960932 +0900
@@ -174,14 +174,22 @@
     ifeq (x86_64, $(shell uname -p))
         BITS=64
     endif
+    ifeq (aarch64, $(shell uname -p))
+        BITS=64
+    endif
 endif
 
 ifeq (32,$(BITS))
     $(error bowtie2 compilation requires a 64-bit platform )
 endif
 
-DEBUG_FLAGS = -O0 -g3 -m64
-RELEASE_FLAGS = -O3 -m64
+ifeq (aarch64, $(shell uname -p))
+    DEBUG_FLAGS = -O0 -g3
+    RELEASE_FLAGS = -O3
+else
+    DEBUG_FLAGS = -O0 -g3 -m64
+    RELEASE_FLAGS = -O3 -m64
+endif
 NOASSERT_FLAGS = -DNDEBUG
 FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
 
diff -ur bowtie-1.2.3.org/ebwt.h bowtie-1.2.3/ebwt.h
--- bowtie-1.2.3.org/ebwt.h	2019-09-26 12:14:35.518559804 +0900
+++ bowtie-1.2.3/ebwt.h	2019-09-26 14:13:12.142637470 +0900
@@ -1957,7 +1957,11 @@
     struct USE_POPCNT_INSTRUCTION {
         inline static int pop64(uint64_t x) {
             int64_t count;
+#ifdef __aarch64__
+            count = __builtin_popcount(x);
+#else
             asm ("popcntq %[x],%[count]\n": [count] "=&r" (count): [x] "r" (x));
+#endif
             return count;
         }
     };
diff -ur bowtie-1.2.3.org/third_party/cpuid.h bowtie-1.2.3/third_party/cpuid.h
--- bowtie-1.2.3.org/third_party/cpuid.h	2019-09-26 12:14:35.548562971 +0900
+++ bowtie-1.2.3/third_party/cpuid.h	2019-09-26 12:17:41.677842567 +0900
@@ -65,6 +65,7 @@
 #define bit_FSGSBASE	(1 << 0)
 #define bit_BMI		(1 << 3)
 
+#ifndef __aarch64__
 #if defined(__i386__) && defined(__PIC__)
 /* %ebx may be the PIC register.  */
 #if __GNUC__ >= 3
@@ -185,3 +186,13 @@
   __cpuid (__level, *__eax, *__ebx, *__ecx, *__edx);
   return 1;
 }
+#endif
+#ifdef __aarch64__ 
+static __inline int
+__get_cpuid (unsigned int __level,
+             unsigned int *__eax, unsigned int *__ebx,
+             unsigned int *__ecx, unsigned int *__edx)
+{
+  return 1;
+}
+#endif