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biology/pooler: Optimise DNA sequencing primer-set combinations

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Optimise combinations of primers and minimise the formation of dimers in
multiplexed PCR.

Primer Pooler can:

* Check through each proposed pool for combinations that are likely to form
  dimers

* Automatically move prospective amplicons between proposed pools to reduce
  dimer formation

* Automatically search the genome sequence to find which amplicons overlap, and
  place their corresponding primers in separate pools

* Optionally keep pool sizes within a specified range

* Handle thousands of primers without being slow (useful for high-throughput
  sequencing applications)

* Do all of the above with degenerate primers too.

WWW: http://ssb22.user.srcf.net/pooler/

PR:             ports/251065
Submitted by:   Silas S. Brown <silas-freebsd@flatline.org.uk>
This commit is contained in:
Jason W. Bacon 2020-11-15 18:50:17 +00:00
parent bf689b58be
commit 018d7f39c9
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=555418
4 changed files with 52 additions and 0 deletions
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1
biology/Makefile
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@ -114,6 +114,7 @@
SUBDIR += phyml
SUBDIR += picard-tools
SUBDIR += plink
SUBDIR += pooler
SUBDIR += primer3
SUBDIR += prodigal
SUBDIR += prodigy-lig

26
biology/pooler/Makefile Normal file
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@ -0,0 +1,26 @@
# $FreeBSD$
PORTNAME= pooler
DISTVERSIONPREFIX= v
DISTVERSION= 1.75
CATEGORIES= biology
MAINTAINER= ssb22@cam.ac.uk
COMMENT= Optimise DNA sequencing primer-set combinations
LICENSE= APACHE20
LICENSE_FILE= ${WRKDIR}/${GH_PROJECT}-${PORTVERSION}/LICENSE
USES= compiler:openmp
USE_GITHUB= yes
GH_ACCOUNT= ssb22
GH_PROJECT= PrimerPooler
WRKSRC_SUBDIR= pooler
CFLAGS+= -fopenmp
INSTALL_TARGET= install-strip
PLIST_FILES= bin/pooler man/man1/pooler.1.gz
.include <bsd.port.mk>

3
biology/pooler/distinfo Normal file
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@ -0,0 +1,3 @@
TIMESTAMP = 1605447867
SHA256 (ssb22-PrimerPooler-v1.75_GH0.tar.gz) = 7d0c0c6b58724a42100b1019995385568747f3b5620b09b297d3e77758c35818
SIZE (ssb22-PrimerPooler-v1.75_GH0.tar.gz) = 125999

22
biology/pooler/pkg-descr Normal file
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@ -0,0 +1,22 @@
Optimise combinations of primers and minimise the formation of dimers in
multiplexed PCR.
Primer Pooler can:
* Check through each proposed pool for combinations that are likely to form
dimers
* Automatically move prospective amplicons between proposed pools to reduce
dimer formation
* Automatically search the genome sequence to find which amplicons overlap, and
place their corresponding primers in separate pools
* Optionally keep pool sizes within a specified range
* Handle thousands of primers without being slow (useful for high-throughput
sequencing applications)
* Do all of the above with degenerate primers too.
WWW: http://ssb22.user.srcf.net/pooler/