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)