diff --git a/biology/wfa2-lib/Makefile b/biology/wfa2-lib/Makefile
index 2300f379ec6f..a8a95a8229d4 100644
--- a/biology/wfa2-lib/Makefile
+++ b/biology/wfa2-lib/Makefile
@@ -1,21 +1,20 @@
 PORTNAME=		wfa2-lib
 DISTVERSIONPREFIX=	v
-DISTVERSION=		2.3.2
-PORTREVISION=		1
+DISTVERSION=		2.3.4
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Exact gap-affine algorithm using homology to accelerate alignment
 WWW=		https://github.com/smarco/WFA2-lib
 
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 USES=		cmake pkgconfig
 USE_GITHUB=	yes
 USE_LDCONFIG=	yes
 
 GH_ACCOUNT=	smarco
 GH_PROJECT=	WFA2-lib
 
 .include <bsd.port.mk>
diff --git a/biology/wfa2-lib/distinfo b/biology/wfa2-lib/distinfo
index 09a5d3555324..ab50e1352a95 100644
--- a/biology/wfa2-lib/distinfo
+++ b/biology/wfa2-lib/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1675088499
-SHA256 (smarco-WFA2-lib-v2.3.2_GH0.tar.gz) = 310e3886506ab57d04205cdf5fed3ef31969ce39e9c6d341fd5c8a0d4aa0830b
-SIZE (smarco-WFA2-lib-v2.3.2_GH0.tar.gz) = 4150874
+TIMESTAMP = 1695995337
+SHA256 (smarco-WFA2-lib-v2.3.4_GH0.tar.gz) = 3a02d19b45c7efcdcabdd956421b1e449e771fca0b0f072e02d7aa65ebb29f23
+SIZE (smarco-WFA2-lib-v2.3.4_GH0.tar.gz) = 4224505
diff --git a/biology/wfa2-lib/files/patch-CMakeLists.txt b/biology/wfa2-lib/files/patch-CMakeLists.txt
index 8b71ad656f0a..5be0031f15f4 100644
--- a/biology/wfa2-lib/files/patch-CMakeLists.txt
+++ b/biology/wfa2-lib/files/patch-CMakeLists.txt
@@ -1,11 +1,11 @@
---- CMakeLists.txt.orig	2023-01-31 15:02:27 UTC
+--- CMakeLists.txt.orig	2023-09-29 13:47:52 UTC
 +++ CMakeLists.txt
 @@ -55,7 +55,7 @@ if(NOT CMAKE_BUILD_TYPE)
  endif()
  
  if (${CMAKE_BUILD_TYPE} MATCHES Release)
 -  set(OPTIMIZE_FLAGS "${OPTIMIZE_FLAGS} -march=native -D_FILE_OFFSET_BITS=64")
 +  set(OPTIMIZE_FLAGS "${OPTIMIZE_FLAGS} -D_FILE_OFFSET_BITS=64")
  endif()
  
  if ((${CMAKE_BUILD_TYPE} MATCHES Release) OR (${CMAKE_BUILD_TYPE} MATCHES RelWithDebInfo))
diff --git a/biology/wfa2-lib/files/patch-wavefront_wavefront__extend__kernels.c b/biology/wfa2-lib/files/patch-wavefront_wavefront__extend__kernels.c
new file mode 100644
index 000000000000..c46271b7a21e
--- /dev/null
+++ b/biology/wfa2-lib/files/patch-wavefront_wavefront__extend__kernels.c
@@ -0,0 +1,11 @@
+--- wavefront/wavefront_extend_kernels.c.orig	2023-09-29 17:25:17 UTC
++++ wavefront/wavefront_extend_kernels.c
+@@ -29,7 +29,7 @@
+  * DESCRIPTION: WFA module for the "extension" of exact matches
+  */
+ 
+-#include <endian.h>
++#include <sys/endian.h>
+ 
+ #include "wavefront_extend_kernels.h"
+ #include "wavefront_termination.h"
diff --git a/biology/wfa2-lib/pkg-plist b/biology/wfa2-lib/pkg-plist
index 235ff54015ca..2fa4ac482adc 100644
--- a/biology/wfa2-lib/pkg-plist
+++ b/biology/wfa2-lib/pkg-plist
@@ -1,46 +1,53 @@
 include/wfa2lib/alignment/affine2p_penalties.h
 include/wfa2lib/alignment/affine_penalties.h
 include/wfa2lib/alignment/cigar.h
 include/wfa2lib/alignment/linear_penalties.h
 include/wfa2lib/alignment/score_matrix.h
+include/wfa2lib/bindings/cpp/WFAligner.hpp
 include/wfa2lib/system/mm_allocator.h
 include/wfa2lib/system/mm_stack.h
 include/wfa2lib/system/profiler_counter.h
 include/wfa2lib/system/profiler_timer.h
 include/wfa2lib/utils/bitmap.h
 include/wfa2lib/utils/commons.h
 include/wfa2lib/utils/dna_text.h
 include/wfa2lib/utils/heatmap.h
 include/wfa2lib/utils/sequence_buffer.h
-include/wfa2lib/utils/string_padded.h
 include/wfa2lib/utils/vector.h
 include/wfa2lib/wavefront/wavefront.h
 include/wfa2lib/wavefront/wavefront_align.h
 include/wfa2lib/wavefront/wavefront_aligner.h
 include/wfa2lib/wavefront/wavefront_attributes.h
 include/wfa2lib/wavefront/wavefront_backtrace.h
 include/wfa2lib/wavefront/wavefront_backtrace_buffer.h
 include/wfa2lib/wavefront/wavefront_backtrace_offload.h
 include/wfa2lib/wavefront/wavefront_bialign.h
 include/wfa2lib/wavefront/wavefront_bialigner.h
 include/wfa2lib/wavefront/wavefront_components.h
 include/wfa2lib/wavefront/wavefront_compute.h
 include/wfa2lib/wavefront/wavefront_compute_affine.h
 include/wfa2lib/wavefront/wavefront_compute_affine2p.h
 include/wfa2lib/wavefront/wavefront_compute_edit.h
 include/wfa2lib/wavefront/wavefront_compute_linear.h
 include/wfa2lib/wavefront/wavefront_debug.h
 include/wfa2lib/wavefront/wavefront_display.h
 include/wfa2lib/wavefront/wavefront_extend.h
+include/wfa2lib/wavefront/wavefront_extend_kernels.h
+include/wfa2lib/wavefront/wavefront_extend_kernels_avx.h
 include/wfa2lib/wavefront/wavefront_heuristic.h
 include/wfa2lib/wavefront/wavefront_offset.h
 include/wfa2lib/wavefront/wavefront_pcigar.h
 include/wfa2lib/wavefront/wavefront_penalties.h
 include/wfa2lib/wavefront/wavefront_plot.h
+include/wfa2lib/wavefront/wavefront_sequences.h
 include/wfa2lib/wavefront/wavefront_slab.h
+include/wfa2lib/wavefront/wavefront_termination.h
 include/wfa2lib/wavefront/wavefront_unialign.h
 include/wfa2lib/wavefront/wfa.h
 include/wfa2lib/wavefront/wfa.hpp
 lib/libwfa2.a
 lib/libwfa2.so
 lib/libwfa2.so.0
+lib/libwfa2cpp.a
+lib/libwfa2cpp.so
+lib/libwfa2cpp.so.0