abacas - close gaps in genomic alignments from short reads

Property Value
Distribution Debian 10 (Buster)
Repository Debian Main amd64
Package filename abacas_1.3.1-5_all.deb
Package name abacas
Package version 1.3.1
Package release 5
Package architecture all
Package type deb
Category field::biology field::biology:bioinformatics implemented-in::perl interface::commandline interface::text-mode role::program science scope::utility
Homepage http://abacas.sourceforge.net/
License -
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Download size 23.71 KB
Installed size 109.00 KB
ABACAS (Algorithm Based Automatic Contiguation of Assembled Sequences)
intends to rapidly contiguate (align, order, orientate), visualize and
design primers to close gaps on shotgun assembled contigs based on a
reference sequence.
ABACAS uses MUMmer to find alignment positions and identify syntenies
of assembled contigs against the reference. The output is then processed
to generate a pseudomolecule taking overlapping contigs and gaps in to
account. ABACAS generates a comparison file that can be used to
visualize ordered and oriented contigs in ACT. Synteny is represented by
red bars where colour intensity decreases with lower values of percent
identity between comparable blocks. Information on contigs such as the
orientation, percent identity, coverage and overlap with other contigs
can also be visualized by loading the outputted feature file on ACT.


Package Version Architecture Repository
abacas_1.3.1-5_all.deb 1.3.1 all Debian Main
abacas - - -


Name Value
mummer -


Type URL
Mirror ftp.br.debian.org
Binary Package abacas_1.3.1-5_all.deb
Source Package abacas

Install Howto

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




2018-10-04 - Andreas Tille <tille@debian.org>
abacas (1.3.1-5) unstable; urgency=medium
[ Steffen Moeller ]
* debian/upstream/metadata:
- References to registries
- yamllint clean
* debian/control: improved description
[ Andreas Tille ]
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
2017-09-21 - Andreas Tille <tille@debian.org>
abacas (1.3.1-4) unstable; urgency=medium
[ Steffen Moeller ]
* Introduced EDAM annotation
[ Andreas Tille ]
* Move packaging from SVN to Git
* Standards-Version: 4.1.0 (no changes needed)
* debhelper 10
2016-01-25 - Andreas Tille <tille@debian.org>
abacas (1.3.1-3) unstable; urgency=medium
* Moved debian/upstream to debian/upstream/metadata
* cme fix dpkg-control
2013-10-25 - Andreas Tille <tille@debian.org>
abacas (1.3.1-2) unstable; urgency=low
* debian/upstream: Added citation information
* debian/control:
- cme fix dpkg-control
- debhelper 9
- canocoal Vcs URLs
* debian/copyright: DEP5
2011-03-21 - Andreas Tille <tille@debian.org>
abacas (1.3.1-1) unstable; urgency=low
* Initial release (Closes: #619100)

See Also

Package Description
abcde_2.9.3-1_all.deb A Better CD Encoder
abci_0.0~git20170124.0.f94ae5e-2+b33_amd64.deb Tendermint's Serverside Blockchain API
abcm2ps_8.14.2-0.2_amd64.deb Translates ABC music description files to PostScript
abcmidi_20190101-1_amd64.deb converter from ABC to MIDI format and back
abe-data_1.1+dfsg-3_all.deb side-scrolling game named "Abe's Amazing Adventure" -- data
abe_1.1+dfsg-3_amd64.deb side-scrolling game named "Abe's Amazing Adventure"
abgate_1.1.9-1_amd64.deb LV2 noise gate plugin
abi-compliance-checker_2.3-0.2_all.deb tool to compare ABI compatibility of shared C/C++ library versions
abi-dumper_1.1-1_all.deb tool to dump ABI of an ELF object containing DWARF debug info
abi-monitor_1.12-2_all.deb monitor ABI of shared libraries
abi-tracker_1.11-1_all.deb visualize ABI changes of a C/C++ library
abicheck_1.2-5_all.deb binary compatibility checking tool
abigail-doc_1.5-1_all.deb ABI Generic Analysis and Instrumentation Library (documentation)
abigail-tools_1.5-1_amd64.deb ABI Generic Analysis and Instrumentation Library (tools)
abinit-data_8.8.4-2_all.deb package for electronic structure calculations (Data files)