The attached patch appears to fix the build in Ubuntu.
diff -Nru minimap2-2.17+dfsg/debian/changelog minimap2-2.17+dfsg/debian/changelog
--- minimap2-2.17+dfsg/debian/changelog 2020-07-07 21:32:26.000000000 +1200
+++ minimap2-2.17+dfsg/debian/changelog 2020-09-15 12:34:50.000000000 +1200
@@ -1,3 +1,10 @@
+minimap2 (2.17+dfsg-11ubuntu1) groovy; urgency=medium
+
+ * d/patches/python-sse4-arch.patch: Only pass -msse4.1 to the compiler on
+ amd64.
+
+ -- Michael Hudson-Doyle <michael.hud...@ubuntu.com> Tue, 15 Sep 2020 12:34:50 +1200
+
minimap2 (2.17+dfsg-11) unstable; urgency=medium
* Add lintian-override
diff -Nru minimap2-2.17+dfsg/debian/control minimap2-2.17+dfsg/debian/control
--- minimap2-2.17+dfsg/debian/control 2020-07-07 21:32:26.000000000 +1200
+++ minimap2-2.17+dfsg/debian/control 2020-09-15 12:34:50.000000000 +1200
@@ -1,5 +1,6 @@
Source: minimap2
-Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org>
+Maintainer: Ubuntu Developers <ubuntu-devel-disc...@lists.ubuntu.com>
+XSBC-Original-Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org>
Uploaders: Andreas Tille <ti...@debian.org>
Section: science
Priority: optional
diff -Nru minimap2-2.17+dfsg/debian/patches/python-sse4-arch.patch minimap2-2.17+dfsg/debian/patches/python-sse4-arch.patch
--- minimap2-2.17+dfsg/debian/patches/python-sse4-arch.patch 1970-01-01 12:00:00.000000000 +1200
+++ minimap2-2.17+dfsg/debian/patches/python-sse4-arch.patch 2020-09-15 12:34:50.000000000 +1200
@@ -0,0 +1,11 @@
+--- a/setup.py
++++ b/setup.py
+@@ -26,7 +26,7 @@
+ if platform.machine() in ["aarch64", "arm64"]:
+ include_dirs.append("sse2neon/")
+ extra_compile_args.extend(['-ftree-vectorize', '-DKSW_SSE2_ONLY', '-D__SSE2__'])
+-else:
++elif platform.machine() == "x86_64":
+ extra_compile_args.append('-msse4.1') # WARNING: ancient x86_64 CPUs don't have SSE4
+
+ def readme():
diff -Nru minimap2-2.17+dfsg/debian/patches/series minimap2-2.17+dfsg/debian/patches/series
--- minimap2-2.17+dfsg/debian/patches/series 2020-07-07 21:32:26.000000000 +1200
+++ minimap2-2.17+dfsg/debian/patches/series 2020-09-15 12:34:42.000000000 +1200
@@ -3,3 +3,4 @@
simde
ar.patch
link_mappy_to_libminimap.patch
+python-sse4-arch.patch
