abacas
close gaps in genomic alignments from short reads
Command lineScience
Not tested on a device yet. What that means
Commands in the package
abacas
About abacas
From Debian's package description
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.
From Debian's description of the abacas package, under that package's license.
Dependencies
Depends on
Recommends
Related apps
- bowtie2ultrafast memory-efficient short read alignerCommand line
- bowtieUltrafast memory-efficient short read alignerCommand line
- hisat2graph-based alignment of short nucleotide reads to many genomesCommand line
- macsModel-based Analysis of ChIP-Seq on short reads sequencersCommand line
- bbmapBBTools genomic aligner and other tools for short sequencesCommand line
- dascrubberalignment-based scrubbing pipeline for DNA sequencing readsCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the abacas package, under that package's license.
- Description: Debian's description of the abacas package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
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