diff --git a/CMakeLists.txt b/CMakeLists.txt
index cd5b978..0a3ea09 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -3,6 +3,20 @@ project(KMC VERSION 1.0
   DESCRIPTION "SBWT fork of KMC"
   LANGUAGES CXX)
 
+find_package(Git QUIET)
+if(GIT_FOUND AND EXISTS "${PROJECT_SOURCE_DIR}/.git")
+  option(GIT_SUBMODULE "Check submodules during build" ON)
+  if(GIT_SUBMODULE)
+    message(STATUS "Submodule update")
+    execute_process(COMMAND ${GIT_EXECUTABLE} submodule update --init --recursive
+      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+      RESULT_VARIABLE GIT_SUBMOD_RESULT)
+    if(NOT GIT_SUBMOD_RESULT EQUAL "0")
+      message(FATAL_ERROR "git submodule update --init --recursive failed with ${GIT_SUBMOD_RESULT}, please checkout submodules")
+    endif()
+  endif()
+endif()
+
 if(NOT ZLIB)
   find_library(ZLIB NAMES z PATHS ${CMAKE_CURRENT_SOURCE_DIR}/kmc_tools/libs/ REQUIRED)
 endif()
@@ -11,24 +25,28 @@ if(NOT BZIP2)
   find_library(BZIP2 NAMES bz2 PATHS ${CMAKE_CURRENT_SOURCE_DIR}/kmc_tools/libs/ REQUIRED)
 endif()
 
-
 set(KMC_MAIN_DIR ${CMAKE_CURRENT_SOURCE_DIR}/kmc_core)
 set(KMC_CLI_DIR ${CMAKE_CURRENT_SOURCE_DIR}/kmc_CLI)
 set(KMC_API_DIR ${CMAKE_CURRENT_SOURCE_DIR}/kmc_api)
 set(KMC_TOOLS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/kmc_tools)
 
 if(APPLE)
-  add_library(RADULS_SSE2_OBJS OBJECT ${KMC_MAIN_DIR}/raduls_sse2.cpp)
-  target_compile_options(RADULS_SSE2_OBJS PRIVATE -msse2 -O3 -m64 -static-libgcc -static-libstdc++ -pthread -std=c++14)
-
-  add_library(RADULS_SSE41_OBJS OBJECT ${KMC_MAIN_DIR}/raduls_sse41.cpp)
-  target_compile_options(RADULS_SSE41_OBJS PRIVATE -msse4.1 -O3 -m64 -static-libgcc -static-libstdc++ -pthread -std=c++14)
-
-  add_library(RADULS_AVX_OBJS OBJECT ${KMC_MAIN_DIR}/raduls_avx.cpp)
-  target_compile_options(RADULS_AVX_OBJS PRIVATE -mavx -O3 -m64 -static-libgcc -static-libstdc++ -pthread -std=c++14)
-
-  add_library(RADULS_AVX2_OBJS OBJECT ${KMC_MAIN_DIR}/raduls_avx2.cpp)
-  target_compile_options(RADULS_AVX2_OBJS PRIVATE -mavx2 -O3 -m64 -static-libgcc -static-libstdc++ -pthread -std=c++14)
+  if(CMAKE_SYSTEM_PROCESSOR MATCHES "arm64")
+    add_library(RADULS_NEON_OBJS OBJECT ${KMC_MAIN_DIR}/raduls_neon.cpp)
+    target_compile_options(RADULS_NEON_OBJS PRIVATE -march=armv8-a -O3 -static-libgcc -static-libstdc++ -pthread -std=c++14)
+  else()
+    add_library(RADULS_SSE2_OBJS OBJECT ${KMC_MAIN_DIR}/raduls_sse2.cpp)
+    target_compile_options(RADULS_SSE2_OBJS PRIVATE -msse2 -O3 -m64 -static-libgcc -static-libstdc++ -pthread -std=c++14)
+
+    add_library(RADULS_SSE41_OBJS OBJECT ${KMC_MAIN_DIR}/raduls_sse41.cpp)
+    target_compile_options(RADULS_SSE41_OBJS PRIVATE -msse4.1 -O3 -m64 -static-libgcc -static-libstdc++ -pthread -std=c++14)
+
+    add_library(RADULS_AVX_OBJS OBJECT ${KMC_MAIN_DIR}/raduls_avx.cpp)
+    target_compile_options(RADULS_AVX_OBJS PRIVATE -mavx -O3 -m64 -static-libgcc -static-libstdc++ -pthread -std=c++14)
+
+    add_library(RADULS_AVX2_OBJS OBJECT ${KMC_MAIN_DIR}/raduls_avx2.cpp)
+    target_compile_options(RADULS_AVX2_OBJS PRIVATE -mavx2 -O3 -m64 -static-libgcc -static-libstdc++ -pthread -std=c++14)
+  endif()
 else()
   add_library(RADULS_SSE2_OBJS OBJECT ${KMC_MAIN_DIR}/raduls_sse2.cpp)
   target_compile_options(RADULS_SSE2_OBJS PRIVATE -msse2 -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14)
@@ -43,15 +61,23 @@ else()
   target_compile_options(RADULS_AVX2_OBJS PRIVATE -mavx2 -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14)
 endif()
 
+# KKMC CLI OBJECTS
+
 add_library(KMC_CLI_OBJS OBJECT ${KMC_CLI_DIR}/kmc.cpp)
 
+# KFF OBJECTS
+
 add_library(KFF_OBJS OBJECT ${KMC_MAIN_DIR}/kff_writer.cpp)
 
+# KMC API OBJECTS
+
 add_library(KMC_API_OBJS OBJECT
   ${KMC_API_DIR}/mmer.cpp
   ${KMC_API_DIR}/kmc_file.cpp
   ${KMC_API_DIR}/kmer_api.cpp)
 
+# KMC CORE OBJECTS
+
 add_library(KMC_CORE_OBJS OBJECT
   ${KMC_MAIN_DIR}/mem_disk_file.cpp
   ${KMC_MAIN_DIR}/rev_byte.cpp
@@ -68,6 +94,8 @@ add_library(KMC_CORE_OBJS OBJECT
   ${KMC_MAIN_DIR}/kb_collector.cpp
   ${KMC_MAIN_DIR}/kmc_runner.cpp)
 
+# KMC TOOLS OBJECTS
+
 add_library(KMC_TOOLS_OBJS OBJECT
   ${KMC_TOOLS_DIR}/kmer_file_header.cpp
   ${KMC_TOOLS_DIR}/kmc_tools.cpp
@@ -84,20 +112,39 @@ add_library(KMC_TOOLS_OBJS OBJECT
   ${KMC_API_DIR}/kmc_file.cpp
   ${KMC_API_DIR}/kmer_api.cpp)
 
-add_library(kmc_core STATIC
-  $<TARGET_OBJECTS:KMC_CORE_OBJS>
-  $<TARGET_OBJECTS:KMC_API_OBJS>
-  $<TARGET_OBJECTS:KFF_OBJS>
-  $<TARGET_OBJECTS:RADULS_SSE2_OBJS>
-  $<TARGET_OBJECTS:RADULS_SSE41_OBJS>
-  $<TARGET_OBJECTS:RADULS_AVX_OBJS>
-  $<TARGET_OBJECTS:RADULS_AVX2_OBJS>)
+# KMC CORE
+
+if(CMAKE_SYSTEM_PROCESSOR MATCHES "arm64")
+  add_library(kmc_core STATIC
+    $<TARGET_OBJECTS:KMC_CORE_OBJS>
+    $<TARGET_OBJECTS:KMC_API_OBJS>
+    $<TARGET_OBJECTS:KFF_OBJS>
+    $<TARGET_OBJECTS:RADULS_NEON_OBJS>)
+else()
+  add_library(kmc_core STATIC
+    $<TARGET_OBJECTS:KMC_CORE_OBJS>
+    $<TARGET_OBJECTS:KMC_API_OBJS>
+    $<TARGET_OBJECTS:KFF_OBJS>
+    $<TARGET_OBJECTS:RADULS_SSE2_OBJS>
+    $<TARGET_OBJECTS:RADULS_SSE41_OBJS>
+    $<TARGET_OBJECTS:RADULS_AVX_OBJS>
+    $<TARGET_OBJECTS:RADULS_AVX2_OBJS>)
+endif()
+
 if(APPLE)
-  target_compile_options(kmc_core PRIVATE -O3 -m64 -static-libgcc -static-libstdc++ -pthread -std=c++14)
-  target_link_libraries(kmc_core PRIVATE
-    ${ZLIB}
-    ${BZIP2})
-  target_link_options(kmc_core PRIVATE -lm -static-libgcc -static-libstdc++ -O3 -pthread -std=c++14)
+  if(CMAKE_SYSTEM_PROCESSOR MATCHES "arm64")
+    target_compile_options(kmc_core PRIVATE -O3 -static-libgcc -static-libstdc++ -pthread -std=c++14)
+    target_link_libraries(kmc_core PRIVATE
+      ${ZLIB}
+      ${BZIP2})
+    target_link_options(kmc_core PRIVATE -lm -static-libgcc -static-libstdc++ -O3 -pthread -std=c++14)
+  else()
+    target_compile_options(kmc_core PRIVATE -O3 -m64 -static-libgcc -static-libstdc++ -pthread -std=c++14)
+    target_link_libraries(kmc_core PRIVATE
+      ${ZLIB}
+      ${BZIP2})
+    target_link_options(kmc_core PRIVATE -lm -static-libgcc -static-libstdc++ -O3 -pthread -std=c++14)
+  endif()
 else()
   target_compile_options(kmc_core PRIVATE -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14)
   target_link_libraries(kmc_core PRIVATE
@@ -106,16 +153,27 @@ else()
   target_link_options(kmc_core PRIVATE -lm -static -O3 -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14)
 endif()
 
+# KMC TOOLS
+
 add_library(kmc_tools STATIC
   $<TARGET_OBJECTS:KMC_TOOLS_OBJS>
   $<TARGET_OBJECTS:KMC_API_OBJS>
   $<TARGET_OBJECTS:KFF_OBJS>)
+
 if(APPLE)
-  target_compile_options(kmc_tools PRIVATE -O3 -m64 -static-libgcc -static-libstdc++ -pthread -std=c++14)
-  target_link_libraries(kmc_tools PRIVATE
-    ${ZLIB}
-    ${BZIP2})
-  target_link_options(kmc_tools PRIVATE -lm -static-libgcc -static-libstdc++ -O3 -pthread -std=c++14)
+  if(CMAKE_SYSTEM_PROCESSOR MATCHES "arm64")
+    target_compile_options(kmc_tools PRIVATE -O3 -static-libgcc -static-libstdc++ -pthread -std=c++14)
+    target_link_libraries(kmc_tools PRIVATE
+      ${ZLIB}
+      ${BZIP2})
+    target_link_options(kmc_tools PRIVATE -lm -static-libgcc -static-libstdc++ -O3 -pthread -std=c++14)
+  else()
+    target_compile_options(kmc_tools PRIVATE -O3 -m64 -static-libgcc -static-libstdc++ -pthread -std=c++14)
+    target_link_libraries(kmc_tools PRIVATE
+      ${ZLIB}
+      ${BZIP2})
+    target_link_options(kmc_tools PRIVATE -lm -static-libgcc -static-libstdc++ -O3 -pthread -std=c++14)
+  endif()
 else()
   target_compile_options(kmc_tools PRIVATE -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14)
   target_link_libraries(kmc_tools PRIVATE