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Source: abacas
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>,
Nilesh Patra <npatra974@gmail.com>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13)
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/abacas
Vcs-Git: https://salsa.debian.org/med-team/abacas.git
Homepage: http://abacas.sourceforge.net/
Rules-Requires-Root: no
Package: abacas
Architecture: all
Depends: ${perl:Depends},
${misc:Depends},
mummer
Suggests: abacas-examples
Recommends: primer3
Description: close gaps in genomic alignments from short reads
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: abacas-examples
Architecture: all
Depends: ${misc:Depends}
Enhances: abacas
Description: sample data for abacas to close gaps in genomic alignments
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.
.
This package contains a test data set as well as sample scripts
running some test suite provided by Debian also as autopkgtest.
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