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)

1.0                                              September 2015                                        DBDUST(1)