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[ Source: kmer  ]

Package: atac (0~20150903+r2013-6)

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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.

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Download atac

Download for all available architectures
Architecture Package Size Installed Size Files
alpha (unofficial port) 424.3 kB3,087.0 kB [list of files]
amd64 379.3 kB2,763.0 kB [list of files]
arm64 362.8 kB2,547.0 kB [list of files]
armel 359.2 kB2,533.0 kB [list of files]
armhf 361.8 kB2,145.0 kB [list of files]
hppa (unofficial port) 478.4 kB3,086.0 kB [list of files]
i386 403.4 kB3,001.0 kB [list of files]
m68k (unofficial port) 404.3 kB2,913.0 kB [list of files]
mips 442.0 kB3,139.0 kB [list of files]
mips64el 401.9 kB3,117.0 kB [list of files]
mipsel 452.6 kB3,139.0 kB [list of files]
powerpcspe (unofficial port) 418.4 kB3,529.0 kB [list of files]
ppc64 (unofficial port) 407.9 kB3,868.0 kB [list of files]
ppc64el 429.0 kB3,867.0 kB [list of files]
riscv64 (unofficial port) 411.6 kB2,461.0 kB [list of files]
s390x 348.2 kB2,815.0 kB [list of files]
sh4 (unofficial port) 463.6 kB2,693.0 kB [list of files]
sparc64 (unofficial port) 335.0 kB2,744.0 kB [list of files]
x32 (unofficial port) 385.0 kB2,717.0 kB [list of files]