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biology/preseq: Predict yield of distinct reads from a genomic library

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The preseq package is aimed at predicting the yield of distinct reads
from a genomic library from an initial sequencing experiment. The
estimates can then be used to examine the utility of further
sequencing, optimize the sequencing depth, or to screen multiple
libraries to avoid low complexity samples.
This commit is contained in:
Jason W. Bacon 2024-11-22 14:35:51 -06:00
parent 246ad4a653
commit af7a74db00
5 changed files with 47 additions and 0 deletions
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1
biology/Makefile
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@ -156,6 +156,7 @@
SUBDIR += picard-tools
SUBDIR += plink
SUBDIR += pooler
SUBDIR += preseq
SUBDIR += primer3
SUBDIR += prodigal
SUBDIR += prodigy-lig

21
biology/preseq/Makefile Normal file
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@ -0,0 +1,21 @@
PORTNAME= preseq
DISTVERSION= 3.2.0
CATEGORIES= biology
# Github-generated distfiles are incomplete
MASTER_SITES= https://github.com/smithlabcode/preseq/releases/download/v${DISTVERSION}/
MAINTAINER= jwb@FreeBSD.org
COMMENT= Predict yield of distinct reads from a genomic library
WWW= https://github.com/smithlabcode/preseq
LICENSE= GPLv3
LICENSE_FILE= ${WRKSRC}/LICENSE
LIB_DEPENDS= libhts.so:biology/htslib
USES= localbase
GNU_CONFIGURE= yes
CONFIGURE_ARGS= --enable-hts
.include <bsd.port.mk>

3
biology/preseq/distinfo Normal file
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@ -0,0 +1,3 @@
TIMESTAMP = 1732301093
SHA256 (preseq-3.2.0.tar.gz) = 95b81c9054e0d651de398585c7e96b807ad98f0bdc541b3e46665febbe2134d9
SIZE (preseq-3.2.0.tar.gz) = 6488708

5
biology/preseq/pkg-descr Normal file
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@ -0,0 +1,5 @@
The preseq package is aimed at predicting the yield of distinct reads
from a genomic library from an initial sequencing experiment. The
estimates can then be used to examine the utility of further
sequencing, optimize the sequencing depth, or to screen multiple
libraries to avoid low complexity samples.

17
biology/preseq/pkg-plist Normal file
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@ -0,0 +1,17 @@
bin/preseq
bin/to-mr
include/GenomicRegion.hpp
include/MappedRead.hpp
include/OptionParser.hpp
include/QualityScore.hpp
include/bisulfite_utils.hpp
include/chromosome_utils.hpp
include/cigar_utils.hpp
include/dna_four_bit.hpp
include/htslib_wrapper_deprecated.hpp
include/sam_record.hpp
include/sim_utils.hpp
include/smithlab_os.hpp
include/smithlab_utils.hpp
include/zlib_wrapper.hpp
lib/libsmithlab_cpp.a