atac
genome assembly-to-assembly comparison
Command lineScience
Not tested on a device yet. What that means
Commands in the package
atac
About atac
From Debian's package description
atac computes a one-to-one pairwise alignment of large DNA sequences. It first finds the unique k-mers in each sequence, chains them to larger blocks, and fills in spaces between blocks. It was written primarily to transfer annotations between different assemblies of the human genome.
The output is a set of ungapped 'matches', and a set of gapped 'runs' formed from the matches. Each match or run associates one sequence with the other sequence. The association is 'unique', in that there is no other (sizeable) associations for either sequence. Thus, large repeats and duplications are not present in the output - they appear as unmapped regions.
Though the output is always pairwise, atac can cache intermediate results to speed a comparisons of multiple sequences.
This package is part of the Kmer suite.
From Debian's description of the atac package, under that package's license.
Dependencies
Depends on
Recommends
kmer-examples
Related apps
- sim4dbbatch spliced alignment of cDNA sequences to a target genomeCommand line
- leaffbiological sequence library utilities and applicationsCommand line
- merylin- and out-of-core kmer counting and utilitiesCommand line
- roaryhigh speed stand alone pan genome pipelineCommand line
- last-aligngenome-scale comparison of biological sequencesCommand line
- pilonautomated genome assembly improvement and variant detection toolCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the atac package, under that package's license.
- Description: Debian's description of the atac 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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