diff --git a/biology/mashmap/Makefile b/biology/mashmap/Makefile
index ab77f63f41c4..eaaca49903b5 100644
--- a/biology/mashmap/Makefile
+++ b/biology/mashmap/Makefile
@@ -1,32 +1,35 @@
 PORTNAME=	mashmap
 DISTVERSIONPREFIX=	v
-DISTVERSION=	3.1.2
+DISTVERSION=	3.1.3
 CATEGORIES=	biology
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Fast approximate aligner for long DNA sequences
 WWW=		https://github.com/marbl/MashMap
 
 LICENSE=	PD
 LICENSE_FILE=	${WRKSRC}/LICENSE.txt
 
 BROKEN_i386=	compilation fails: fatal error: unknown type name '__uint128_t'
 BROKEN_powerpc=	compilation fails: fatal error: unknown type name '__uint128_t'
 
 LIB_DEPENDS=	libgsl.so:math/gsl \
 		libhts.so:biology/htslib
 
-USES=		cmake compiler:c++17-lang localbase:ldflags
+USES=		cmake compiler:c++17-lang localbase:ldflags pkgconfig
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	marbl
 GH_PROJECT=	MashMap
 
+CMAKE_ON=	USE_HTSLIB
+CMAKE_OFF=	OPTIMIZE_FOR_NATIVE
+
 OPTIONS_DEFINE=		NATIVE
 
 NATIVE_CMAKE_BOOL=	OPTIMIZE_FOR_NATIVE
 
 PLIST_FILES=	bin/mashmap \
 		bin/mashmap-align
 
 .include <bsd.port.mk>
diff --git a/biology/mashmap/distinfo b/biology/mashmap/distinfo
index 9e6f5286225b..8830cb134d4f 100644
--- a/biology/mashmap/distinfo
+++ b/biology/mashmap/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1701829049
-SHA256 (marbl-MashMap-v3.1.2_GH0.tar.gz) = cf9bb085cc85b0f1b91f4fc45a907cff536099a4a82031f1e112259e24ba5976
-SIZE (marbl-MashMap-v3.1.2_GH0.tar.gz) = 25919468
+TIMESTAMP = 1704429274
+SHA256 (marbl-MashMap-v3.1.3_GH0.tar.gz) = 7719dd6b3c25e650e16218252eaae7dbf424a10890d717ec3ad0920b102fd05a
+SIZE (marbl-MashMap-v3.1.3_GH0.tar.gz) = 25919699