diff --git a/biology/bowtie2/Makefile b/biology/bowtie2/Makefile
index a09862b29506..8ef489a65a53 100644
--- a/biology/bowtie2/Makefile
+++ b/biology/bowtie2/Makefile
@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	bowtie2
-PORTVERSION=	2.2.9
+PORTVERSION=	2.3.0
 DISTVERSIONPREFIX=	v
 CATEGORIES=	biology
 
@@ -12,6 +12,8 @@ COMMENT=	Ultrafast, memory-efficient short read aligner
 LICENSE=	GPLv3+
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
+LIB_DEPENDS+=	libtbb.so:devel/tbb
+
 # May also work on other 64-bit platforms, but untested
 ONLY_FOR_ARCHS=	amd64
 USES=		gmake perl5 python shebangfix
diff --git a/biology/bowtie2/distinfo b/biology/bowtie2/distinfo
index 32a39c53fefa..2c1808146d4f 100644
--- a/biology/bowtie2/distinfo
+++ b/biology/bowtie2/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1475861880
-SHA256 (BenLangmead-bowtie2-v2.2.9_GH0.tar.gz) = af940f77fc36aabea90d3d865724fd7ec7e250788d2d2f793c45c713d16ae5ee
-SIZE (BenLangmead-bowtie2-v2.2.9_GH0.tar.gz) = 5815106
+TIMESTAMP = 1487550143
+SHA256 (BenLangmead-bowtie2-v2.3.0_GH0.tar.gz) = 9804fddf36233f3f92c11e2250224de3395790cf35c8280c66387075df078221
+SIZE (BenLangmead-bowtie2-v2.3.0_GH0.tar.gz) = 5810016
diff --git a/biology/bowtie2/files/patch-Makefile b/biology/bowtie2/files/patch-Makefile
index be8a43586cec..6c4919530320 100644
--- a/biology/bowtie2/files/patch-Makefile
+++ b/biology/bowtie2/files/patch-Makefile
@@ -1,4 +1,4 @@
---- Makefile.orig	2016-02-11 17:20:57 UTC
+--- Makefile.orig	2016-12-30 15:40:06 UTC
 +++ Makefile
 @@ -21,8 +21,8 @@
  # Makefile for bowtie, bowtie2-build, bowtie2-inspect
@@ -11,7 +11,34 @@
  
  INC =
  GCC_PREFIX = $(shell dirname `which gcc`)
-@@ -169,7 +169,7 @@ SSE_FLAG=-msse2 
+@@ -62,6 +62,8 @@ ifeq (1, $(POPCNT_CAPABILITY))
+     INC += -I third_party
+ endif
+ 
++INC += -I ${LOCALBASE}/include
++
+ MM_DEF =
+ 
+ ifeq (1,$(BOWTIE_MM))
+@@ -75,7 +77,7 @@ ifeq (1,$(BOWTIE_SHARED_MEM))
+ endif
+ 
+ PTHREAD_PKG =
+-PTHREAD_LIB =
++PTHREAD_LIB = 
+ 
+ #if we're not using TBB, then we can't use queuing locks
+ ifeq (1,$(NO_TBB))
+@@ -94,7 +96,7 @@ endif
+ 
+ #default is to use Intel TBB
+ ifneq (1,$(NO_TBB))
+-	LIBS = $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy
++	LIBS = $(PTHREAD_LIB) -L${LOCALBASE}/lib -ltbb -ltbbmalloc
+ 	override EXTRA_FLAGS += -DWITH_TBB
+ else
+ 	LIBS = $(PTHREAD_LIB)
+@@ -185,7 +187,7 @@ SSE_FLAG=-msse2
  
  DEBUG_FLAGS    = -O0 -g3 -m64 $(SSE_FLAG)
  DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
diff --git a/biology/bowtie2/files/patch-aligner__result.cpp b/biology/bowtie2/files/patch-aligner__result.cpp
new file mode 100644
index 000000000000..4a6c9f729522
--- /dev/null
+++ b/biology/bowtie2/files/patch-aligner__result.cpp
@@ -0,0 +1,13 @@
+https://github.com/BenLangmead/bowtie2/issues/81
+
+--- aligner_result.cpp.orig	2016-12-30 15:40:06 UTC
++++ aligner_result.cpp
+@@ -1130,7 +1130,7 @@ bool AlnFlags::printYF(BTString& o, bool
+ 	else if(!nfilt_  ) flag = "NS";
+ 	else if(!scfilt_ ) flag = "SC";
+ 	else if(!qcfilt_ ) flag = "QC";
+-	if(flag > 0) {
++	if(*flag != '\0') {
+ 		if(!first) o.append('\t');
+ 		o.append("YF:Z:");
+ 		o.append(flag);