pywgsim is a modified version of the wgsim short read simulator. The
code for wgsim has been modified to allow visualizing the simulated
mutations as a GFF file.
Biolibc-tools is a collection of simple fast, memory-efficient,
programs for processing biological data. These are simple programs
built on biolibc that are not complex enough to warrant a separate
project.
BFC is a standalone high-performance tool for correcting sequencing
errors from Illumina sequencing data. It is specifically designed for
high-coverage whole-genome human data, though also performs well for
small genomes.
FLASH (Fast Length Adjustment of SHort reads) is a very fast and
accurate software tool to merge paired-end reads from next-generation
sequencing experiments. FLASH is designed to merge pairs of reads when
the original DNA fragments are shorter than twice the length of reads.
The resulting longer reads can significantly improve genome assemblies.
They can also improve transcriptome assembly when FLASH is used to
merge RNA-seq data.
The ont_fast5_api is a simple interface to HDF5 files of the Oxford
Nanopore .fast5 file format. It provides:
o Implementation of the fast5 file schema using h5py library
o Methods to interact with and reflect the fast5 file schema
o Tools to convert between multi_read and single_read formats
o Tools to compress/decompress raw data in files
ErmineJ performs analyses of gene sets in high-throughput genomics data
such as gene expression profiling studies. A typical goal is to
determine whether particular biological pathways are "doing something
interesting" in an experiment that generates long lists of candidates.
The software is designed to be used by biologists with little or no
informatics background (but if you do, you might be interested in the
CLI or the R support).
MMseqs2 (Many-against-Many sequence searching) is a software suite to search
and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source
GPL-licensed software implemented in C++ for FreeBSD, Linux, MacOS, and (via
via cygwin) Windows. The software is designed to run on multiple cores and
servers and exhibits very good scalability. MMseqs2 can run 10000 times
faster than BLAST. At 100 times its speed it achieves almost the same
sensitivity. It can perform profile searches with the same sensitivity as
PSI-BLAST at over 400 times its speed.
SRA tools is a toolkit for using data in the INSDC Sequence Read Archives.
SRAs operated by International Nucleotide Sequence Database Collaboration
houses sequence reads and alignments generated by "next-gen" sequencers.
This port is a bit convoluted due to the fact that the sra-tools build
requires access to the ncbi-vdb source tree. Hence, ncbi-vdb is treated
as a submodule here rather than a separate library port. We are working
with upstream with hope for long-term improvements.
Biostar-Tools is a metaport for installing all the tools necessary to work
through the Biostar Handbook, except for bedGrapToBigWig, which has license
restrictions. If you need bedGraphToBigWig, run
cd /usr/ports/biology/ucsc-userapps && make install clean
Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
Peaks are provided in a BED file sorted by chromosome and position.
The GFF must be sorted by chromosome and position, with gene-level
features separated by ### tags and each gene organized into
subfeatures such as transcripts and exons. This is the default for
common data sources.
Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected
databases (publication, sequence, structure, gene, variation, expression, etc.)
from a UNIX terminal window.
Genetic variant annotation and functional effect prediction toolbox. It
annotates and predicts the effects of genetic variants on genes and proteins
(such as amino acid changes).
This package includes BBMap, a short read aligner, as well as various other
bioinformatic tools. It is written in pure Java, can run on any platform, and
has no dependencies other than Java being installed (compiled for Java 6 and
higher). All tools are efficient and multithreaded.
Sequence reading library developed by the Ribosomal Database Project. It can
handle genbank, embl, fasta, fastq, sff and sto files, can read from files or
streams, and can handle indexing files.
CrossMap is a program for genome coordinates conversion between different
assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used
file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF, MAF VCF,
and gVCF.
A python extension, written in C, for quick access to bigBed files and access
to and creation of bigWig files. This extension uses libBigWig for local and
remote file access.
2021-04-01 ftp/wzdftpd: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 astro/roadmap: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 games/cosmo: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 games/bomberinstinct: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 games/drm: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 games/bygfoot: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 games/cre: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 irc/hybserv: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 irc/xaric: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 mail/elmo: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 misc/cave: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 security/bugs: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 security/dmitry: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 security/doorman: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 shells/esh: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 sysutils/cpu: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 textproc/libcrm114: No known users, dead upstream
2021-04-01 x11/wmmatrix: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 x11/wmxss: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 x11/tycoon: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 x11/xgrab: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 x11/xbanner: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 x11/bricons: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 x11/xmon: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 games/cavezofphear: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 astro/saoimage: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/ksmp3play: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/jamin: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/musicbox-tag-editor: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/nspmod: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/cdplay: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/gimmix: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/ghostess: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/wmrecord: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/toolame: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/shout: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 biology/grappa: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 biology/phylip: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 biology/lagan: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 cad/varkon: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 cad/transcalc: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 comms/seyon: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 comms/efax: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 converters/vda2fbd: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 converters/shftool: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 devel/openzz: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 devel/sourcenav: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 devel/gb: Unmaintained and dead upstream
2021-04-01 dns/checkdns: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 dns/inadyn-mt: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 editors/gate: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 editors/thoteditor: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 emulators/cinc: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 emulators/e-uae: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 emulators/dtcyber: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 ftp/jftpgw: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 ftp/pureadmin: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-02 textproc/hs-pandoc-citeproc: Integrated into textproc/hs-pandoc
vcf2hap is a simple tool for generating a .hap file from a VCF. The .hap file
is required by haplohseq. vcf2hap is extremely fast and requires a trivial
amount of memory regardless of the size of the VCF file.
ad2vdf extracts allelic depth info from a SAM stream and adds it to a
corresponding single-sample VCF file. SAM input is read via stdin and the VCF
input file is taken as a command-line argument. This allows expensive BAM/CRAM
decoding to be performed in parallel by a separate samtools process.
Vcf-split splits a multi-sample VCF into single-sample VCFs, writing thousands
of output files simultaneously. Parsing the TOPMed human chromosome 1 BCF
with bcftools takes two days, so extracting the 137,977 samples one at a time
or using thousands of parallel readers of the same file is impractical.
Vcf-split solves this by generating thousands of single-sample outputs during
a single sweep through the multi-sample input.
Biolibc is a library of fast, memory-efficient, low-level functions for
processing biological data. Like libc, it consists of numerous disparate,
general-purpose functions which could be used by a wide variety of
applications. These include functions for streaming common file formats such
as SAM and VCF, string functions specific to bioinformatics, etc.
Generate random genomic data in FASTA/FASTQ, SAM, or VCF format, suitable for
small academic examples or test inputs of arbitrary size. Output can be piped
directly to programs or redirected to a file and edited to taste.
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>
2020-09-15 audio/abraca: Uses deprecated version of python
2020-09-15 audio/ardour5: Uses deprecated version of python
2020-09-15 audio/cplay: Uses deprecated version of python
2020-09-15 audio/cpp-xmms2: Uses deprecated version of python
2020-09-15 audio/p5-xmms2: Uses deprecated version of python
2020-09-15 biology/haplohseq: Uses deprecated version of python
2020-09-15 biology/tophat: Uses deprecated version of python
2020-09-15 chinese/ibus-array: Uses deprecated version of python
2020-09-15 comms/congruity: Uses deprecated version of python
2020-09-15 comms/libbtbb: Uses deprecated version of python
2020-09-15 comms/quisk: Uses deprecated version of python
2020-09-15 databases/mtools-mongodb: Uses deprecated version of python
2020-09-15 databases/mydbf2mysql: Uses deprecated version of python
2020-09-15 databases/ntdb: Uses deprecated version of python
2020-09-15 databases/pgloader: Uses deprecated version of python
2020-09-15 databases/pgtune: Uses deprecated version of python
2020-09-15 databases/postgresql-libpqxx3: Uses deprecated version of python
2020-09-15 databases/postgresql-libpqxx4: Uses deprecated version of python
2020-09-15 databases/py-sqlite3dbm: Uses deprecated version of python
2020-09-15 databases/pydbx: Uses deprecated version of python
2020-09-15 databases/pyspatialite: Uses deprecated version of python
2020-09-15 deskutils/ljcharm: Uses deprecated version of python
2020-09-15 deskutils/mat: Uses deprecated version of python
2020-09-15 devel/aap: Uses deprecated version of python
2020-09-15 devel/apr2: Uses deprecated version of python
2020-09-15 devel/bbfreeze-loader: Uses deprecated version of python
2020-09-15 devel/bicyclerepair: Uses deprecated version of python
2020-09-15 devel/bzrtools: Uses deprecated version of python
2020-09-15 devel/codeville: Uses deprecated version of python
2020-09-15 devel/cvs2svn: Uses deprecated version of python
2020-09-15 devel/cx_Freeze: Uses deprecated version of python
2020-09-15 devel/euca2ools: Uses deprecated version of python
2020-09-15 devel/evolution-gconf-tools: Uses deprecated version of python
2020-09-15 devel/git-bzr-ng: Uses deprecated version of python
2020-09-15 devel/git-cvs: Uses deprecated version of python
2020-09-15 devel/git-remote-hg: Uses deprecated version of python
2020-09-15 devel/grumpy: Uses deprecated version of python
2020-09-15 devel/hg-git: Uses deprecated version of python
2020-09-15 devel/libnxt: Uses deprecated version of python
2020-09-15 devel/libredblack: Uses deprecated version of python
2020-09-15 devel/llvm-cheri: Uses deprecated version of python
2020-09-15 devel/phpsh: Uses deprecated version of python
2020-09-15 devel/py-backports.shutil_which: Uses deprecated version of python
2020-09-15 devel/py-notify: Uses deprecated version of python
2020-09-15 devel/py-pybloomfiltermmap: Uses deprecated version of python
2020-09-15 devel/py-qserve: Uses deprecated version of python
2020-09-15 devel/py-subvertpy: Uses deprecated version of python
2020-09-15 devel/py_static_check: Uses deprecated version of python
2020-09-15 devel/pyst: Uses deprecated version of python
2020-09-15 devel/runsnakerun: Uses deprecated version of python
2020-09-15 devel/tailor: Uses deprecated version of python
2020-09-15 devel/uatraits: Uses deprecated version of python
2020-09-15 dns/nsec3walker: Uses deprecated version of python
2020-09-15 dns/sshfp: Uses deprecated version of python
2020-09-15 editors/medit: Uses deprecated version of python
2020-09-15 emulators/dynagen: Uses deprecated version of python
2020-09-15 emulators/wxmupen64plus: Uses deprecated version of python
2020-09-15 games/diameter: Uses deprecated version of python
2020-09-15 games/kiki: Uses deprecated version of python
2020-09-15 games/lightyears: Uses deprecated version of python
2020-09-15 games/outerspace: Uses deprecated version of python
2020-09-15 games/pachi-game-engine: Uses deprecated version of python
2020-09-15 graphics/caffe: Uses deprecated version of python
2020-09-15 graphics/cloudcompare: Uses deprecated version of python
2020-09-15 graphics/kudu: Uses deprecated version of python
2020-09-15 graphics/pecomato: Uses deprecated version of python
2020-09-15 graphics/py-editobj: Uses deprecated version of python
2020-09-15 graphics/py-mayavi: Uses deprecated version of python
2020-09-15 graphics/pymorph: Uses deprecated version of python
2020-09-15 graphics/tilecache: Uses deprecated version of python
2020-09-15 graphics/uniconvertor: Uses deprecated version of python
2020-09-15 japanese/mailman: Uses deprecated version of python
2020-09-15 java/eclipse-pydev: Uses deprecated version of python
2020-09-15 lang/cdent: Uses deprecated version of python
2020-09-15 lang/julia06: Uses deprecated version of python
2020-09-15 lang/julia07: Uses deprecated version of python
2020-09-15 lang/julia11: Uses deprecated version of python
2020-09-15 lang/tinypy: Uses deprecated version of python
2020-09-15 mail/cleanup-maildir: Uses deprecated version of python
2020-09-15 mail/courier-pythonfilter: Uses deprecated version of python
2020-09-15 mail/getmail: Uses deprecated version of python
2020-09-15 mail/muttils: Uses deprecated version of python
2020-09-15 mail/nohtml: Uses deprecated version of python
2020-09-15 mail/offlineimap: Uses deprecated version of python
2020-09-15 mail/openemm2015: Uses deprecated version of python
2020-09-15 math/blitz++: Uses deprecated version of python
2020-09-15 math/openfst: Uses deprecated version of python
2020-09-15 math/py-fpconst: Uses deprecated version of python
2020-09-15 misc/hb: Uses deprecated version of python
2020-09-15 misc/mtail: Uses deprecated version of python
2020-09-15 misc/wotsap: Uses deprecated version of python
2020-09-15 multimedia/freevo: Uses deprecated version of python
2020-09-15 multimedia/quodlibet: Uses deprecated version of python
2020-09-15 multimedia/tovid: Uses deprecated version of python
2020-09-15 net/ceph13: Uses deprecated version of python
2020-09-15 net/cloud-init-azure: Uses deprecated version of python
2020-09-15 net/exabgp: Uses deprecated version of python
2020-09-15 net/exaddos: Uses deprecated version of python
2020-09-15 net/fb: Uses deprecated version of python
2020-09-15 net/flent: Uses deprecated version of python
2020-09-15 net/flowgrep: Uses deprecated version of python
2020-09-15 net/googlecl: Uses deprecated version of python
2020-09-15 net/mininet: Uses deprecated version of python
2020-09-15 net/nfs-ganesha: Uses deprecated version of python
2020-09-15 net/opensips: Uses deprecated version of python
2020-09-15 net/py-python-ntlm: Uses deprecated version of python
2020-09-15 net/splatd: Uses deprecated version of python
2020-09-15 net-im/centerim-devel: Uses deprecated version of python
2020-09-15 net-im/fugu: Uses deprecated version of python
2020-09-15 net-im/proxy65: Uses deprecated version of python
2020-09-15 net-mgmt/crmsh: Uses deprecated version of python
2020-09-15 net-mgmt/librenms-agent: Uses deprecated version of python
2020-09-15 net-p2p/couchpotato: Uses deprecated version of python
2020-09-15 news/rawdog: Uses deprecated version of python
2020-09-15 ports-mgmt/portell: Uses deprecated version of python
2020-09-15 print/biblio-py: Uses deprecated version of python
2020-09-15 science/brian: Uses deprecated version of python
2020-09-15 science/paraview: Uses deprecated version of python
2020-09-15 security/arm: Uses deprecated version of python
2020-09-15 security/ismtp: Uses deprecated version of python
2020-09-15 security/py-halberd: Uses deprecated version of python
2020-09-15 security/switzerland: Uses deprecated version of python
2020-09-15 security/tsshbatch: Uses deprecated version of python
2020-09-15 shells/lshell: Uses deprecated version of python
2020-09-15 sysutils/abck: Uses deprecated version of python
2020-09-15 sysutils/condor: Uses deprecated version of python
2020-09-15 sysutils/farbot: Uses deprecated version of python
2020-09-15 sysutils/fusefs-wikipediafs: Uses deprecated version of python
2020-09-15 sysutils/heartbeat: Uses deprecated version of python
2020-09-15 sysutils/isomd5sum: Uses deprecated version of python
2020-09-15 sysutils/py-stdiff: Uses deprecated version of python
2020-09-15 sysutils/tren: Uses deprecated version of python
2020-09-15 textproc/doclifter: Uses deprecated version of python
2020-09-15 textproc/ibus-el: Uses deprecated version of python
2020-09-15 textproc/p5-WWW-Google-SiteMap: Deprecated upstream, see textproc/p5-Search-Sitemap
2020-09-15 textproc/plover: Uses deprecated version of python
2020-09-15 textproc/py-esmre: Uses deprecated version of python
2020-09-15 textproc/py-libxslt: Uses deprecated version of python
2020-09-15 textproc/py-pdfminer: Uses deprecated version of python
2020-09-15 textproc/translate-toolkit: Uses deprecated version of python
2020-09-15 www/bluefish: Uses deprecated version of python
2020-09-15 www/calendarserver: Uses deprecated version of python
2020-09-15 www/geeknote: Uses deprecated version of python
2020-09-15 www/go-appengine-sdk: Uses deprecated version of python
2020-09-15 www/google-appengine: Uses deprecated version of python
2020-09-15 www/libhpack: Uses deprecated version of python
2020-09-15 www/mkapachepw: Uses deprecated version of python
2020-09-15 www/mod_pagespeed: Uses deprecated version of python
2020-09-15 www/mod_python35: Uses deprecated version of python
2020-09-15 www/py-qp: Uses deprecated version of python
2020-09-15 www/py-url: Uses deprecated version of python
2020-09-15 www/pyblosxom: Uses deprecated version of python
2020-09-15 www/pyjamas: Uses deprecated version of python
2020-09-15 www/roundup: Uses deprecated version of python
2020-09-15 www/varnish-libvmod-awsrest: Uses deprecated version of python
2020-09-15 www/waccess: Uses deprecated version of python
2020-09-15 www/wadcomblog: Uses deprecated version of python
2020-09-15 www/webcheck: Uses deprecated version of python
2020-09-15 www/woof: Uses deprecated version of python
2020-09-15 x11-drivers/xf86-video-qxl: uses deprecated version of python
2020-09-15 x11-fm/twander: Uses deprecated version of python
2020-09-15 x11-wm/compizconfig-python: Uses deprecated version of python
2020-09-15 x11-wm/fvwm-crystal: Uses deprecated version of python
2020-08-26 audio/timidity++-tcltk: Broken for more than 6 months
2020-08-26 biology/pbcopper: Broken for more than 6 months
2020-08-26 devel/ace: Broken for more than 6 months
2020-08-26 devel/bin86: Broken for more than 6 months
2020-08-26 devel/erlang-oserl: Broken for more than 6 months
2020-08-20 emulators/qemu40: Please consider using qemu or qemu41
2020-08-26 games/linux-darwinia-demo: Broken for more than 6 months
2020-08-26 games/linux-defcon: Broken for more than 6 months
2020-08-26 games/linux-uplink-demo: Broken for more than 6 months
2020-08-26 games/xevil: Broken for more than 6 months
2020-08-26 games/xminesweep: Broken for more than 6 months
2020-08-26 graphics/backfract: Broken for more than 6 months
2020-08-26 japanese/kanjipad: Broken for more than 6 months
2020-08-26 japanese/xdtp: Broken for more than 6 months
2020-08-26 korean/hpscat: Broken for more than 6 months
2020-08-26 math/barvinok: Broken for more than 6 months
2020-08-26 math/openmesh: Broken for more than 6 months
2020-08-26 math/rehearse: Broken for more than 6 months
2020-08-26 net/hinfo: Broken for more than 6 months
2020-08-26 science/fleur: Broken for more than 6 months
2020-08-26 science/lm: Broken for more than 6 months
2020-08-26 security/ddos_scan: Broken for more than 6 months
2020-08-26 security/gag: Broken for more than 6 months
2020-08-26 security/py-keystone: Broken for more than 6 months
2020-08-26 sysutils/mono-kmod: mastersite disappeared, unfetchable
2020-08-26 x11-themes/gtk-cleanice-engine: Broken for more than 6 months
2020-08-26 x11-wm/aewm: Broken for more than 6 months
