abacas - Algorithm Based Automatic Contiguation of Assembled Sequences

Property Value
Distribution Debian 8 (Jessie)
Repository Debian Main amd64
Package name abacas
Package version 1.3.1
Package release 2
Package architecture all
Package type deb
Installed size 135 B
Download size 23.36 KB
Official Mirror ftp.br.debian.org
ABACAS is intended 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 comparision 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_1.3.1-2_all.deb 1.3.1 all Debian Main
abacas - - -


Name Value
mummer -


Type URL
Binary Package abacas_1.3.1-2_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




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

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abcmidi_20141016-1_amd64.deb converter from ABC to MIDI format and back
abe-data_1.1+dfsg-1_all.deb Side-scrolling game named "Abe's Amazing Adventure"
abe_1.1+dfsg-1_amd64.deb Side-scrolling game named "Abe's Amazing Adventure"
abgate_1.1.7-1_amd64.deb LV2 noise gate plugin
abi-compliance-checker_1.99.9-2_all.deb tool to compare ABI compatibility of shared C/C++ library versions
abi-dumper_0.99.8-1_all.deb tool to dump ABI of an ELF object containing DWARF debug info
abicheck_1.2-5_all.deb binary compatibility checking tool
abinit-data_7.8.2-2_all.deb package for electronic structure calculations (Data files)
abinit-doc_7.8.2-2_all.deb package for electronic structure calculations (Documentation)
abinit_7.8.2-2_amd64.deb package for electronic structure calculations
abiword-common_3.0.0-8_all.deb efficient, featureful word processor with collaboration -- common files
abiword-plugin-grammar_3.0.0-8+b1_amd64.deb grammar checking plugin for AbiWord
abiword-plugin-mathview_3.0.0-8+b1_amd64.deb equation editor plugin for AbiWord