abacas

close gaps in genomic alignments from short reads

Install

All systems
curl cmd.cat/abacas.sh
Debian Debian
apt-get install abacas
Ubuntu
apt-get install abacas
image/svg+xml Kali Linux
apt-get install abacas
Windows (WSL2)
sudo apt-get update sudo apt-get install abacas
Raspbian
apt-get install abacas

abacas

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.