Package: atac (0~20150903+r2013-9)

[ Source: kmer  ]

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

• 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 (>= 2.38)

  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 (>= 3.5)

  GCC support library

• 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 (<< 3.13)

  dep: python3 (>= 3.12~)

• dep: python3.12

  Interactive high-level object-oriented language (version 3.12)

• rec: kmer-examples

  sample data for kmer suite of tools for DNA sequence analysis

Download atac

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Architecture	Package Size	Installed Size	Files
armel	349.3 kB	2,514.0 kB	[list of files]