diff --git a/biology/bowtie2/Makefile b/biology/bowtie2/Makefile
index 198cf295e73e..2cd89b18642b 100644
--- a/biology/bowtie2/Makefile
+++ b/biology/bowtie2/Makefile
@@ -1,55 +1,66 @@
 PORTNAME=		bowtie2
 DISTVERSIONPREFIX=	v
 DISTVERSION=		2.4.2
 PORTREVISION=		4
 CATEGORIES=		biology perl5 python
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Ultrafast, memory-efficient short read aligner
 
 LICENSE=	GPLv3+
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 # Requires a 64-bit processor and depends on hard-coded SSE instructions
 # Experimental support for AARCH64 as of 2.3.5
-ONLY_FOR_ARCHS=	aarch64 amd64
+ONLY_FOR_ARCHS=	aarch64 amd64 powerpc64le
 LIB_DEPENDS=	libtbb.so:devel/onetbb
 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=	nemequ:simde:422ed9c: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 100d7cba6fb8..57c4443eb8df 100644
--- a/biology/bowtie2/distinfo
+++ b/biology/bowtie2/distinfo
@@ -1,3 +1,5 @@
-TIMESTAMP = 1604617529
+TIMESTAMP = 1618499065
 SHA256 (BenLangmead-bowtie2-v2.4.2_GH0.tar.gz) = ea33a1562faf759b21b3a905e20b87a3524ac4e53af8cd723d9a9f31ee159c8a
 SIZE (BenLangmead-bowtie2-v2.4.2_GH0.tar.gz) = 10590144
+SHA256 (nemequ-simde-422ed9c_GH0.tar.gz) = 3e7e962b499212cdddcaeca973d1c15d71a4b620afb46113d936ce5c3a8236ba
+SIZE (nemequ-simde-422ed9c_GH0.tar.gz) = 332230
diff --git a/biology/bowtie2/files/patch-Makefile b/biology/bowtie2/files/patch-Makefile
index 092870a96abf..f082b4abb0d3 100644
--- a/biology/bowtie2/files/patch-Makefile
+++ b/biology/bowtie2/files/patch-Makefile
@@ -1,39 +1,39 @@
---- Makefile.orig	2020-11-05 23:04:50 UTC
+--- Makefile.orig	2020-10-06 03:46:41 UTC
 +++ Makefile
 @@ -24,7 +24,7 @@
  PREFIX := /usr/local
  bindir := $(PREFIX)/bin
  
 -ARCH := $(shell uname -m)
 +ARCH := $(shell uname -p)
  LDLIBS := -lz
  GCC_PREFIX := $(shell dirname `which gcc`)
  GCC_SUFFIX :=
 @@ -201,22 +201,22 @@ endif
  
  BITS := 32
  SSE_FLAG := -msse2
 -ifeq (x86_64,$(shell uname -m))
 +ifeq (x86_64,$(shell uname -p))
    BITS := 64
 -else ifeq (amd64,$(shell uname -m))
 +else ifeq (amd64,$(shell uname -p))
    BITS := 64
 -else ifeq (aarch64,$(shell uname -m))
 +else ifeq (aarch64,$(shell uname -p))
    BITS := 64
    SSE_FLAG :=
    CXXFLAGS += -fopenmp-simd
    CPPFLAGS += -Ithird_party/simde
 -else ifeq (s390x,$(shell uname -m))
 +else ifeq (s390x,$(shell uname -p))
    BITS := 64
    SSE_FLAG :=
    CXXFLAGS += -fopenmp-simd
    CPPFLAGS += -Ithird_party/simde
    SANITIZER_FLAGS :=
 -else ifeq (ppc64le,$(shell uname -m))
-+else ifeq (ppc64le,$(shell uname -p))
++else ifeq (powerpc64le,$(shell uname -p))
    BITS := 64
    SSE_FLAG :=
    CXXFLAGS += -fopenmp-simd