abacas
close gaps in genomic alignments from short reads
Install
- All systems
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curl cmd.cat/abacas.sh
- Debian
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apt-get install abacas - Ubuntu
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apt-get install abacas - Kali Linux
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apt-get install abacas - Windows (WSL2)
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sudo apt-get updatesudo apt-get install abacas - Raspbian
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apt-get install abacas - Dockerfile
- dockerfile.run/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.