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Package: atac (0~20150903+r2013-8build2)

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

  • depends
  • recommends
  • suggests
  • dep: gnuplot
    Command-line driven interactive plotting program.
    also a virtual package provided by gnuplot-nox, gnuplot-qt, gnuplot-x11
  • dep: leaff
    biological sequence library utilities and applications
  • dep: libc6 (>= 2.34)
    GNU C Library: Shared libraries
    also a virtual package provided by libc6-udeb
  • dep: libfile-which-perl
    Perl module for searching paths for executable programs
  • dep: libgcc-s1 (>= 3.3.1) [not armhf]
    GCC support library
    dep: libgcc-s1 (>= 3.5) [armhf]
  • dep: libstdc++6 (>= 5.2)
    GNU Standard C++ Library v3
  • dep: meryl
    in- and out-of-core kmer counting and utilities
  • dep: perl
    Larry Wall's Practical Extraction and Report Language
  • dep: python3
    interactive high-level object-oriented language (default python3 version)
    dep: python3 (<< 3.11)
    dep: python3 (>= 3.10~)
  • dep: python3.10
    Interactive high-level object-oriented language (version 3.10)
  • rec: kmer-examples
    sample data for kmer suite of tools for DNA sequence analysis

Download atac

Download for all available architectures
Architecture Package Size Installed Size Files
amd64 349.2 kB1842 kB [list of files]
arm64 353.6 kB1658 kB [list of files]
armhf 384.6 kB2059 kB [list of files]
ppc64el 390.4 kB2786 kB [list of files]