diff --git a/biology/bowtie2/Makefile b/biology/bowtie2/Makefile
index 6ca11a69916f..b227373a69b0 100644
--- a/biology/bowtie2/Makefile
+++ b/biology/bowtie2/Makefile
@@ -1,64 +1,64 @@
 PORTNAME=		bowtie2
 DISTVERSIONPREFIX=	v
-DISTVERSION=		2.4.5
+DISTVERSION=		2.5.0
 CATEGORIES=		biology perl5 python
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Ultrafast, memory-efficient short read aligner
 WWW=		https://github.com/BenLangmead/bowtie2
 
 LICENSE=	GPLv3+
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 # Requires a 64-bit processor and depends on hard-coded asm instructions
 ONLY_FOR_ARCHS=	aarch64 amd64 powerpc64 powerpc64le
 RUN_DEPENDS=	bash:shells/bash
 
 USES=		gmake localbase:ldflags perl5 python shebangfix
 USE_PERL5=	run
 USE_GITHUB=	yes
 
 SHEBANG_FILES=	bowtie2 bowtie2-build bowtie2-inspect \
 		scripts/bowtie2-hbb.sh scripts/*.pl
 GH_ACCOUNT=	BenLangmead
 GH_TUPLE=	simd-everywhere:simde-no-tests:f6a0b3b:simde
 
 OPTIONS_DEFINE=	DOCS EXAMPLES
 
 SUB_FILES=	bowtie2-test
 
 .include <bsd.port.options.mk>
 
 .if ${ARCH} != amd64
 post-extract:
 	(cd ${WRKSRC_simde}; \
 		${COPYTREE_SHARE} . ${WRKSRC}/third_party/simde/)
 
 MAKE_ENV=	POPCNT_CAPABILITY=0
 .endif
 
 pre-configure:
 	@${REINPLACE_CMD} \
 		-e 's|^RELEASE_FLAGS|# RELEASE_FLAGS|' \
 		-e 's|tbbmalloc_proxy|tbbmalloc|' \
 		${WRKSRC}/Makefile
 
 post-install:
 	@${MKDIR} ${STAGEDIR}${DATADIR}/scripts
 	${INSTALL_PROGRAM} \
 		${WRKSRC}/bowtie2*-s \
 		${WRKSRC}/bowtie2*-l \
 		${STAGEDIR}${PREFIX}/bin
 	${INSTALL_SCRIPT} \
 		${WRKSRC}/scripts/*.sh \
 		${WRKSRC}/scripts/*.pl \
 		${STAGEDIR}${DATADIR}/scripts
 	${INSTALL_SCRIPT} ${WRKDIR}/bowtie2-test ${STAGEDIR}${PREFIX}/bin
 
 post-install-DOCS-on:
 	(cd ${WRKSRC}/doc && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR})
 
 post-install-EXAMPLES-on:
 	(cd ${WRKSRC}/example && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR})
 
 .include <bsd.port.mk>
diff --git a/biology/bowtie2/distinfo b/biology/bowtie2/distinfo
index afe87ffa42f1..1ebf87291129 100644
--- a/biology/bowtie2/distinfo
+++ b/biology/bowtie2/distinfo
@@ -1,5 +1,5 @@
-TIMESTAMP = 1642699775
-SHA256 (BenLangmead-bowtie2-v2.4.5_GH0.tar.gz) = db101391b54a5e0eeed7469b05aee55ee6299558b38607f592f6b35a7d41dcb6
-SIZE (BenLangmead-bowtie2-v2.4.5_GH0.tar.gz) = 10585723
+TIMESTAMP = 1667400686
+SHA256 (BenLangmead-bowtie2-v2.5.0_GH0.tar.gz) = 55dedeba8bea240d3ce3f46211d6e14310035c1de5a3e9ac33f72f739165fea0
+SIZE (BenLangmead-bowtie2-v2.5.0_GH0.tar.gz) = 10598633
 SHA256 (simd-everywhere-simde-no-tests-f6a0b3b_GH0.tar.gz) = 9874f22afe8a6cd92770aa194df47db3d0963d80ea233a502b0d557f59763eb8
 SIZE (simd-everywhere-simde-no-tests-f6a0b3b_GH0.tar.gz) = 397743
diff --git a/biology/bowtie2/files/patch-Makefile b/biology/bowtie2/files/patch-Makefile
index fb68d5913e52..491fd10e7b79 100644
--- a/biology/bowtie2/files/patch-Makefile
+++ b/biology/bowtie2/files/patch-Makefile
@@ -1,25 +1,29 @@
---- Makefile.orig	2021-05-15 20:10:26 UTC
+--- Makefile.orig	2022-11-02 14:50:38 UTC
 +++ Makefile
 @@ -32,7 +32,7 @@ BOWTIE_SHARED_MEM :=
  
  CXXFLAGS += -std=c++11
  
 -ARCH = $(shell uname -m)
 +ARCH = $(shell uname -p)
  NGS_VER ?= 2.9.2
  VDB_VER ?= 2.9.2-1
  
-@@ -59,11 +59,11 @@ ifneq (,$(findstring Darwin,$(shell uname)))
+@@ -62,7 +62,7 @@ ifneq (,$(findstring Darwin,$(shell uname)))
  endif
  
  BITS := 32
 -ifneq (,$(findstring $(shell uname -m), x86_64 amd64))
 +ifneq (,$(findstring $(shell uname -p), x86_64 amd64))
    BITS := 64
-   SSE_FLAG := -msse2
+   ifeq (1, $(SSE_AVX2))
+ 	SSE_FLAG := -mavx2 -faligned-new -DSSE_AVX2
+@@ -71,7 +71,7 @@ ifneq (,$(findstring $(shell uname -m), x86_64 amd64))
+   endif
+ 
    POPCNT_CAPABILITY ?= 1
 -else ifneq (,$(findstring $(shell uname -m), aarch64 arm64 s390x ppc64 ppc64le))
-+else ifneq (,$(findstring $(shell uname -p), aarch64 arm64 s390x powerpc64 powerpc64le))
++else ifneq (,$(findstring $(shell uname -p), aarch64 arm64 s390x ppc64 ppc64le))
    BITS := 64
    SSE_FLAG :=
    CXXFLAGS += -fopenmp-simd