diff --git a/biology/minimap2/Makefile b/biology/minimap2/Makefile
index eb65d48578c5..dd10b6869afe 100644
--- a/biology/minimap2/Makefile
+++ b/biology/minimap2/Makefile
@@ -1,34 +1,34 @@
 PORTNAME=		minimap2
 DISTVERSIONPREFIX=	v
-DISTVERSION=		2.29
+DISTVERSION=		2.30
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Pairwise aligner for genomic and spliced nucleotide sequences
 WWW=		https://github.com/lh3/minimap2
 
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE.txt
 
 NOT_FOR_ARCHS=		i386 mips powerpc powerpcspe
 NOT_FOR_ARCHS_REASON=	Requires 64-bit processor, except ARM NEON
 
 BUILD_DEPENDS=	simde>0:devel/simde
 
 USES=		gmake localbase
 USE_GITHUB=	yes
 
 GH_ACCOUNT=	lh3
 
 ALL_TARGET=	extra
 INSTALL_TARGET=	install-strip
 
 MAKEFILE=	Makefile.simde
 MAKE_ARGS=	MAN1DIR=${PREFIX}/share/man/man1
 
 CFLAGS+=	-DHAVE_KALLOC
 
 pre-build:
 	${REINPLACE_CMD} -e 's|-msse4.1||g' -e 's|-msse2||g' ${WRKSRC}/Makefile.simde
 
 .include <bsd.port.mk>
diff --git a/biology/minimap2/distinfo b/biology/minimap2/distinfo
index fac01c43c7f5..f7c616549712 100644
--- a/biology/minimap2/distinfo
+++ b/biology/minimap2/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1745154104
-SHA256 (lh3-minimap2-v2.29_GH0.tar.gz) = 008d5e9848b918e4eb09d054aa3d6c272d50e92b8fc8537abf5081a507019718
-SIZE (lh3-minimap2-v2.29_GH0.tar.gz) = 269107
+TIMESTAMP = 1750076274
+SHA256 (lh3-minimap2-v2.30_GH0.tar.gz) = 4e5cd621be2b2685c5c88d9b9b169c7e036ab9fff2f3afe1a1d4091ae3176380
+SIZE (lh3-minimap2-v2.30_GH0.tar.gz) = 269912
diff --git a/biology/minimap2/patch.minimap2 b/biology/minimap2/patch.minimap2
new file mode 100644
index 000000000000..5b7080cb43d3
--- /dev/null
+++ b/biology/minimap2/patch.minimap2
@@ -0,0 +1,31 @@
+diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/minimap2/Makefile /usr/ports/wip/minimap2/Makefile
+--- /usr/ports/biology/minimap2/Makefile	2025-04-20 08:14:09.261908000 -0500
++++ /usr/ports/wip/minimap2/Makefile	2025-06-16 08:07:58.592212000 -0500
+@@ -1,6 +1,6 @@
+ PORTNAME=		minimap2
+ DISTVERSIONPREFIX=	v
+-DISTVERSION=		2.29
++DISTVERSION=		2.30
+ CATEGORIES=		biology
+ 
+ MAINTAINER=	jwb@FreeBSD.org
+diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/minimap2/distinfo /usr/ports/wip/minimap2/distinfo
+--- /usr/ports/biology/minimap2/distinfo	2025-04-20 08:13:48.648889000 -0500
++++ /usr/ports/wip/minimap2/distinfo	2025-06-16 08:07:57.620437000 -0500
+@@ -1,3 +1,3 @@
+-TIMESTAMP = 1745154104
+-SHA256 (lh3-minimap2-v2.29_GH0.tar.gz) = 008d5e9848b918e4eb09d054aa3d6c272d50e92b8fc8537abf5081a507019718
+-SIZE (lh3-minimap2-v2.29_GH0.tar.gz) = 269107
++TIMESTAMP = 1750076274
++SHA256 (lh3-minimap2-v2.30_GH0.tar.gz) = 4e5cd621be2b2685c5c88d9b9b169c7e036ab9fff2f3afe1a1d4091ae3176380
++SIZE (lh3-minimap2-v2.30_GH0.tar.gz) = 269912
+diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/minimap2/pkg-plist /usr/ports/wip/minimap2/pkg-plist
+--- /usr/ports/biology/minimap2/pkg-plist	2024-04-17 17:51:07.042256000 -0500
++++ /usr/ports/wip/minimap2/pkg-plist	2025-06-16 08:07:57.620515000 -0500
+@@ -8,3 +8,6 @@
+ %%DATADIR%%/test/q2.fa
+ %%DATADIR%%/test/t-inv.fa
+ %%DATADIR%%/test/t2.fa
++%%DATADIR%%/test/x3s-aln.txt
++%%DATADIR%%/test/x3s-qry.fa
++%%DATADIR%%/test/x3s-ref.fa
diff --git a/biology/minimap2/pkg-plist b/biology/minimap2/pkg-plist
index 742d1eb1b3f7..9e386df64f48 100644
--- a/biology/minimap2/pkg-plist
+++ b/biology/minimap2/pkg-plist
@@ -1,10 +1,13 @@
 bin/minimap2
 bin/minimap2-lite
 bin/sdust
 share/man/man1/minimap2.1.gz
 %%DATADIR%%/test/MT-human.fa
 %%DATADIR%%/test/MT-orang.fa
 %%DATADIR%%/test/q-inv.fa
 %%DATADIR%%/test/q2.fa
 %%DATADIR%%/test/t-inv.fa
 %%DATADIR%%/test/t2.fa
+%%DATADIR%%/test/x3s-aln.txt
+%%DATADIR%%/test/x3s-qry.fa
+%%DATADIR%%/test/x3s-ref.fa