pbdagcon_0.3+git20161121.0000000+ds-1.1_amd64.deb


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Description

pbdagcon - sequence consensus using directed acyclic graphs

Property Value
Distribution Ubuntu 19.04 (Disco Dingo)
Repository Ubuntu Universe amd64
Package filename pbdagcon_0.3+git20161121.0000000+ds-1.1_amd64.deb
Package name pbdagcon
Package version 0.3+git20161121.0000000+ds
Package release 1.1
Package architecture amd64
Package type deb
Category universe/science
Homepage https://github.com/PacificBiosciences/pbdagcon
License -
Maintainer Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Download size 315.46 KB
Installed size 1.16 MB
pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus)
which is a sequence consensus algorithm based on using directed acyclic
graphs to encode multiple sequence alignment.
It uses the alignment information from blasr to align sequence reads to a
"backbone" sequence. Based on the underlying alignment directed acyclic graph
(DAG), it will be able to use the new information from the reads to find the
discrepancies between the reads and the "backbone" sequences. A dynamic
programming process is then applied to the DAG to find the optimum sequence
of bases as the consensus. The new consensus can be used as a new backbone
sequence to iteratively improve the consensus quality.
While the code is developed for processing PacBio(TM) raw sequence data,
the algorithm can be used for general consensus purpose. Currently, it only
takes FASTA input. For shorter read sequences, one might need to adjust the
blasr alignment parameters to get the alignment string properly.
The code and the underlying graphical data structure have been used for some
algorithm development prototyping including phasing reads and pre-assembly.

Alternatives

Package Version Architecture Repository
pbdagcon - - -

Requires

Name Value
libc6 >= 2.14
libgcc1 >= 1:3.4
libpbseq -
libstdc++6 >= 6

Download

Type URL
Mirror archive.ubuntu.com
Binary Package pbdagcon_0.3+git20161121.0000000+ds-1.1_amd64.deb
Source Package pbdagcon

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install pbdagcon deb package:
    # sudo apt-get install pbdagcon

Files

Path
/usr/bin/dazcon
/usr/bin/pbdagcon
/usr/share/doc/pbdagcon/README.md.gz
/usr/share/doc/pbdagcon/changelog.Debian.gz
/usr/share/doc/pbdagcon/copyright
/usr/share/doc/pbdagcon/examples/filterm4.py
/usr/share/doc/pbdagcon/examples/m4topre.py
/usr/share/doc/pbdagcon/examples/pbdagcon_wf.sh
/usr/share/doc/pbdagcon/examples/q-sense.py
/usr/share/man/man1/pbdagcon.1.gz

Changelog

2019-02-06 - Adrian Bunk <bunk@debian.org>
pbdagcon (0.3+git20161121.0000000+ds-1.1) unstable; urgency=medium
* Non-maintainer upload.
* Remove manual dependencies on libpbbam, version build
dependency on libpbbam-dev to ensure a proper dependency
is generated.
2019-02-04 - Andreas Tille <tille@debian.org>
pbdagcon (0.3+git20161121.0000000+ds-1) unstable; urgency=low
* Team upload
[ Afif Elghraoui ]
* Add README.source
[ Andreas Tille ]
* d/watch: use git mode to detect new upstream commit
* Reimport old source with version number fitting git mode
* d/get-orig-source: checkout submodules for code copy of DALIGNER and
DAZZ_DB which are specific adaptations to pbdagcon
* debhelper 12
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.3.0
* Build-Depends: libpbdata-dev
Closes: #916576
* Secure URI in copyright format
2016-12-21 - Afif Elghraoui <afif@debian.org>
pbdagcon (0.3+20161121+ds-1) unstable; urgency=medium
* New upstream revision (upstream git 87f393f)
* Include repository's submodules
* Base package versioning on program versions indicated in the source code
* Build with pbbam (Closes: #848755)
* Use pbseqlib metapackages as dependencies
* Build dazcon
* Activate build-time tests
* Use debhelper compat 10
2016-10-23 - Afif Elghraoui <afif@debian.org>
pbdagcon (0~20160325+ds-1) unstable; urgency=medium
* Imported Upstream version 0~20160325+ds
(upstream git revision f19aed1)
* Do not use rpath for pbseqlib
* Update patches
* d/rules: update for changes to build system and dependencies
* Do not build dazcon for now (needs additional sources)
* d/copyright: Remove obsolete declarations
2016-08-04 - Afif Elghraoui <afif@debian.org>
pbdagcon (0~20151114+git1d12e13+ds-3) unstable; urgency=low
* Bump Standards-Version to 3.9.8
* Update email address and bump copyright year
* Use encrypted protocols for VCS URLs
* Do not use -isystem while building (Closes: #831105)
2016-01-22 - Afif Elghraoui <afif@ghraoui.name>
pbdagcon (0~20151114+git1d12e13+ds-2) unstable; urgency=medium
* Adjust packaging for differences in pbseqlib organization.
2015-12-11 - Afif Elghraoui <afif@ghraoui.name>
pbdagcon (0~20151114+git1d12e13+ds-1) unstable; urgency=low
* Initial release (Closes: #796644)

See Also

Package Description
pbgenomicconsensus_2.3.2-5_all.deb Pacific Biosciences variant and consensus caller
pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1_all.deb tools for manipulating Pacific Biosciences HDF5 files
pbsim_1.0.3+git20180330.e014b1d+dfsg-1_amd64.deb simulator for PacBio sequencing reads
pbuilder-scripts_22_all.deb Wrapper scripts for pbuilder
pbuilder_0.230.4_all.deb personal package builder for Debian packages
pbzip2_1.1.9-1build1_amd64.deb parallel bzip2 implementation
pcal_4.11.0-3build1_amd64.deb generate Postscript calendars without X
pcalendar_3.4.1-3_all.deb track menstrual cycles and predict fertility periods
pcapfix_1.1.4-2_amd64.deb repairs broken pcap and pcapng files
pcaputils_0.8-1build1_amd64.deb specialized libpcap utilities
pcb-common_4.2.0-2_all.deb printed circuit board (pcb) design program - common files
pcb-gtk_4.2.0-2_amd64.deb printed circuit board (pcb) design program - GTK+ interface
pcb-lesstif_4.2.0-2_amd64.deb printed circuit board (pcb) design program - LessTif interface
pcb-rnd_2.1.1-1_amd64.deb Modular Printed Circuit Board layout tool
pcb2gcode_1.1.4-git20120902-1.1build3_amd64.deb command-line tool for engraving PCBs using CNCs
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