diff --git a/biology/abyss/Makefile b/biology/abyss/Makefile
index fcfdebd8cc9b..6faf6c0094de 100644
--- a/biology/abyss/Makefile
+++ b/biology/abyss/Makefile
@@ -1,41 +1,41 @@
 PORTNAME=	abyss
-DISTVERSION=	2.3.1
-PORTREVISION=	1
+DISTVERSION=	2.3.5
 CATEGORIES=	biology
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Assembly By Short Sequences: parallel, paired-end sequence assembler
 
 LICENSE=	GPLv3
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BROKEN_i386=	result of comparison of constant 18446744073709551615 with expression of type 'size_t', see https://github.com/bcgsc/abyss/issues/310
 
 BUILD_DEPENDS=	${LOCALBASE}/include/boost/version.hpp:devel/boost-libs \
 		ghc:lang/ghc \
 		pandoc:textproc/hs-pandoc # pandoc is required just for one man page: abyss-sealer
 LIB_DEPENDS=	libffi.so:devel/libffi \
-		libgmp.so:math/gmp
+		libgmp.so:math/gmp \
+		libmpich.so:net/mpich # binaries aren't linked with libmpich.so for some reason
 RUN_DEPENDS=	bash:shells/bash \
 		gmake:devel/gmake
 
 USES=		autoreconf compiler:c++11-lang gmake iconv:wchar_t localbase:ldflags shebangfix sqlite
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	bcgsc
 
 SHEBANG_FILES=	bin/${PORTNAME}-* DataBase/abyss-db-txt
 SHEBANG_LANG=	make
 make_OLD_CMD=	/usr/bin/make
 make_CMD=	${PREFIX}/bin/gmake
 
 GNU_CONFIGURE=	yes
 CONFIGURE_ARGS=	--without-sparsehash # configure fails to find std::hash, reported to the ML: https://groups.google.com/forum/#!topic/trans-abyss/SZDBKR5bKxs
 
 OPTIONS_DEFINE=	DOCS
 
 PORTDOCS=	*
 
 PORTSCOUT=	limit:^[0-9\.]*$$ # to ignore alpha-numeric tags
 
 .include <bsd.port.mk>
diff --git a/biology/abyss/distinfo b/biology/abyss/distinfo
index 864687f7f740..82cc32c0fa85 100644
--- a/biology/abyss/distinfo
+++ b/biology/abyss/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1619108885
-SHA256 (bcgsc-abyss-2.3.1_GH0.tar.gz) = b1941d6d975b38d34f41c38b8f4f599fc69d1f37ef3afb71f50318062fb548ea
-SIZE (bcgsc-abyss-2.3.1_GH0.tar.gz) = 1531044
+TIMESTAMP = 1659120367
+SHA256 (bcgsc-abyss-2.3.5_GH0.tar.gz) = 28fb7d75faa2599c3c4d2d2c29d320612ca1539f1772728d1acdfffb4b82dee5
+SIZE (bcgsc-abyss-2.3.5_GH0.tar.gz) = 3511232
diff --git a/biology/abyss/files/patch-Common_city.cc b/biology/abyss/files/patch-Common_city.cc
index 9fc7031b6639..075c215d82d6 100644
--- a/biology/abyss/files/patch-Common_city.cc
+++ b/biology/abyss/files/patch-Common_city.cc
@@ -1,13 +1,13 @@
---- Common/city.cc.orig	2018-09-21 23:44:14 UTC
+--- Common/city.cc.orig	2022-05-11 22:23:32 UTC
 +++ Common/city.cc
-@@ -65,6 +65,10 @@ static uint32 UNALIGNED_LOAD32(const char *p) {
- #define bswap_32(x) OSSwapInt32(x)
- #define bswap_64(x) OSSwapInt64(x)
+@@ -70,6 +70,10 @@ static uint32 UNALIGNED_LOAD32(const char *p) {
+ #define bswap_32(x) bswap32(x)
+ #define bswap_64(x) bswap64(x)
  
 +#elif defined(__FreeBSD__)
 +#include <sys/endian.h>
 +#define bswap_32(x) bswap32(x)
 +#define bswap_64(x) bswap64(x)
  #else
  #include <byteswap.h>
  #endif
diff --git a/biology/abyss/files/patch-RResolver_btllib_include_btllib_status.hpp b/biology/abyss/files/patch-RResolver_btllib_include_btllib_status.hpp
new file mode 100644
index 000000000000..01427a36b2ac
--- /dev/null
+++ b/biology/abyss/files/patch-RResolver_btllib_include_btllib_status.hpp
@@ -0,0 +1,11 @@
+--- RResolver/btllib/include/btllib/status.hpp.orig	2022-07-29 18:56:25 UTC
++++ RResolver/btllib/include/btllib/status.hpp
+@@ -151,7 +151,7 @@ get_strerror()
+   char buf[buflen];
+ // POSIX and GNU implementation of strerror_r differ, even in function signature
+ // and so we need to check which one is used
+-#if __APPLE__ ||                                                               \
++#if __APPLE__ || defined(__FreeBSD__) ||                                                    \
+   ((_POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600) && !_GNU_SOURCE)
+   strerror_r(errno, buf, buflen);
+   return buf;
diff --git a/biology/abyss/pkg-plist b/biology/abyss/pkg-plist
index 3e2d8eba7135..e40d6907f31b 100644
--- a/biology/abyss/pkg-plist
+++ b/biology/abyss/pkg-plist
@@ -1,60 +1,58 @@
 bin/ABYSS
 bin/ABYSS-P
 bin/AdjList
 bin/Consensus
 bin/DAssembler
 bin/DistanceEst
 bin/DistanceEst-ssq
 bin/KAligner
 bin/MergeContigs
 bin/MergePaths
 bin/Overlap
 bin/ParseAligns
 bin/PathConsensus
 bin/PathOverlap
 bin/PopBubbles
 bin/SimpleGraph
 bin/abyss-align
 bin/abyss-bloom
 bin/abyss-bloom-dbg
 bin/abyss-bloom-dist.mk
 bin/abyss-bowtie
 bin/abyss-bowtie2
 bin/abyss-bwa
 bin/abyss-bwamem
 bin/abyss-bwasw
 bin/abyss-db-csv
 bin/abyss-db-txt
 bin/abyss-dida
 bin/abyss-fac
 bin/abyss-fatoagp
 bin/abyss-filtergraph
 bin/abyss-fixmate
 bin/abyss-fixmate-ssq
 bin/abyss-gapfill
 bin/abyss-gc
 bin/abyss-index
 bin/abyss-junction
 bin/abyss-kaligner
 bin/abyss-layout
 bin/abyss-longseqdist
 bin/abyss-map
 bin/abyss-map-ssq
 bin/abyss-mergepairs
 bin/abyss-overlap
 bin/abyss-paired-dbg
+bin/abyss-paired-dbg-mpi
 bin/abyss-pe
 bin/abyss-rresolver-short
 bin/abyss-samtoafg
 bin/abyss-scaffold
 bin/abyss-sealer
 bin/abyss-stack-size
 bin/abyss-tabtomd
 bin/abyss-todot
 bin/abyss-tofastq
 bin/konnector
 bin/logcounter
-man/man1/ABYSS.1.gz
-man/man1/abyss-pe.1.gz
 man/man1/abyss-sealer.1.gz
-man/man1/abyss-tofastq.1.gz