NAME

       DBdust - description

SYNOPSIS

       DBdust [-b] [-wint(64)] [-tdouble(2.)] [-mint(10)] path:db|dam

DESCRIPTION

       Runs  the  symmetric DUST algorithm over the reads in the untrimmed DB path.db or path.dam
       producing a track .path.dust[.anno,.data] that  marks  all  intervals  of  low  complexity
       sequence,  where  the  scan window is of size -w, the threshold for being a low-complexity
       interval is -t, and only perfect intervals of size greater than -m are recorded.   If  the
       -b option is set then the definition of low complexity takes into account the frequency of
       a given base.  The command is incremental if given a DB to which new data has  been  added
       since  it  was last run on the DB, then it will extend the track to include the new reads.
       It is important to set this flag for genomes with a strong AT/GC bias, albeit the code  is
       a  tad  slower.   The  dust  track,  if  present,  is  understood  and  used by DBshow(1),
       DBstats(1), and daligner(1).

       DBdust can also be run over an untriimmed DB block  in  which  case  it  outputs  a  track
       encoding  where  the trace file names contain the block number, e.g.  .FOO.3.dust.anno and
       .FOO.3.dust.data, given FOO.3 on the command line.  We call  this  a  block  track.   This
       permits  job parallelism in block-sized chunks, and the resulting sequence of block tracks
       can then be merged into a track for the entire untrimmed DB with Catrack.

SEE ALSO

       daligner(1)