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

[ 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

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• dep: leaff

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• dep: libc6 (>= 2.34) [not alpha, ia64, sh4]

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  dep: libc6 (>= 2.36) [sh4]

• dep: libc6.1 (>= 2.34) [alpha]

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• dep: libgcc-s1 (>= 3.0) [amd64, arm64, mips64el, ppc64, ppc64el, s390x, x32]

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  dep: libgcc-s1 (>= 3.4) [alpha, riscv64, sparc64]

  dep: libgcc-s1 (>= 3.5) [armel, armhf]

  dep: libgcc-s1 (>= 4.2) [i386, ia64, sh4]

• dep: libgcc-s2 (>= 4.2.1) [m68k]

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• dep: libgcc-s4 (>= 4.1.1) [hppa]

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• dep: libstdc++6 (>= 5.2)

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• dep: libunwind8 [ia64]

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• dep: perl

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  dep: python3 (<< 3.12)

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• rec: kmer-examples

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Download atac

Download for all available architectures

Architecture	Version	Package Size	Installed Size	Files
alpha (unofficial port)	0~20150903+r2013-8+b3	408.7 kB	3,568.0 kB	[list of files]
amd64	0~20150903+r2013-8+b3	369.3 kB	2,713.0 kB	[list of files]
arm64	0~20150903+r2013-8+b3	346.9 kB	3,296.0 kB	[list of files]
armel	0~20150903+r2013-8+b3	339.0 kB	3,275.0 kB	[list of files]
armhf	0~20150903+r2013-8+b3	338.2 kB	2,763.0 kB	[list of files]
hppa (unofficial port)	0~20150903+r2013-8+b3	463.1 kB	3,012.0 kB	[list of files]
i386	0~20150903+r2013-8+b3	402.8 kB	2,971.0 kB	[list of files]
ia64 (unofficial port)	0~20150903+r2013-8+b3	511.8 kB	4,444.0 kB	[list of files]
m68k (unofficial port)	0~20150903+r2013-8+b3	402.6 kB	2,883.0 kB	[list of files]
mips64el	0~20150903+r2013-8+b3	385.8 kB	3,666.0 kB	[list of files]
ppc64 (unofficial port)	0~20150903+r2013-8+b3	389.8 kB	3,809.0 kB	[list of files]
ppc64el	0~20150903+r2013-8+b3	398.5 kB	3,681.0 kB	[list of files]
riscv64 (unofficial port)	0~20150903+r2013-8+b3	391.6 kB	2,408.0 kB	[list of files]
s390x	0~20150903+r2013-8+b3	337.2 kB	2,732.0 kB	[list of files]
sh4 (unofficial port)	0~20150903+r2013-8+b3	449.8 kB	3,403.0 kB	[list of files]
sparc64 (unofficial port)	0~20150903+r2013-8+b3	354.7 kB	23,362.0 kB	[list of files]
x32 (unofficial port)	0~20150903+r2013-8+b3	380.5 kB	2,671.0 kB	[list of files]