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Package: atac (0~20150903+r2013-3)

genome assembly-to-assembly comparison

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.

Other Packages Related to atac

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  • dep: leaff
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  • dep: libc6 (>= 2.14) [amd64]
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    also a virtual package provided by libc6-udeb
    dep: libc6 (>= 2.7) [i386]
  • dep: libfile-which-perl
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  • dep: libgcc1 (>= 1:3.0) [amd64]
    GCC support library
    dep: libgcc1 (>= 1:4.2) [i386]
  • dep: libstdc++6 (>= 5.2)
    GNU Standard C++ Library v3
  • dep: meryl
    in- and out-of-core kmer counting and utilities
  • dep: perl
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  • dep: python
    interactive high-level object-oriented language (default version)
  • dep: python2.7
    Interactive high-level object-oriented language (version 2.7)

Download atac

Download for all available architectures
Architecture Package Size Installed Size Files
amd64 376.2 kB2683 kB [list of files]
i386 417.3 kB3073 kB [list of files]