abacas on Ubuntu 21.10 (Impish Indri)

Last updated: December 07,2022

1. Install abacas package

In this section, we are going to explain the necessary steps to install abacas package:

sudo apt update
sudo apt install abacas

2. Uninstall / Remove abacas package

This guide covers the steps necessary to uninstall abacas package:

sudo apt remove abacas
sudo apt autoclean && sudo apt autoremove

3. Details of abacas package

Package: abacas
Architecture: all
Version: 1.3.1-9
Priority: optional
Section: universe/science
Origin: Ubuntu
Maintainer: Ubuntu Developers
Original-Maintainer: Debian Med Packaging Team
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Installed-Size: 109
Depends: mummer
Recommends: primer3
Suggests: abacas-examples
Filename: pool/universe/a/abacas/abacas_1.3.1-9_all.deb
Size: 24688
MD5sum: 17e1c12e18a7d5cffa8463f88a87da36
SHA1: 6a198994319ee84dfd210379647adde7da8a2dbd
SHA256: 50bb92486998e31b7566fab108671ae4b85213b7fdea4622301a77b901055a55
SHA512: e277cb0be1321bc0a768b0bce54e4ee75f5f136c598ee1c10f995e803be96036cfb89e86ea866a88223cc12b55083b062dddfe21e12bca4be47dc308c1731490
Homepage: http://abacas.sourceforge.net/
Description-en: 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.
Description-md5: 2037379aa4a21c795f2b3f3ba85ac577