Provided by: atac_0~20150903+r2013-3_amd64 
NAME
atac - comparative mapping between genome sequences
SYNOPSIS
atac -meryldir alignment_cache_dir -dir result_dir -id1 seqid1 -seq1 seqfile1.fasta -id2 seqid2
-seq2 seqfile2.fasta
DESCRIPTION
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.
OPTIONS
Run with no options for a list of parameters.
SEE ALSO
leaff(1), /usr/share/doc/atac/README.atac http://kmer.sourceforge.net/wiki/index.php/Getting_Started_with_ATAC November 2016 ATAC(1)