NAME

       gt-repfind - Compute maximal exact matches (and more).

SYNOPSIS

       gt repfind [options] -ii indexname

DESCRIPTION

       -l [value]
           Specify minimum length of matches (default: 0)

       -f [yes|no]
           Compute forward matches (default: yes)

       -r [yes|no]
           Compute reverse matches (default: no)

       -p [yes|no]
           Compute matches on reverse strand (default: no)

       -seedlength [value]
           Specify minimum length of seed (default: 0)

       -maxfreq [value]
           Specify maximal frequency of maximal exact matches in reference sequence (default: 0)

       -extendxdrop [value]
           Extend seed to both sides using xdrop algorithm, optional parameter specifies
           sensitivity (default: 97)

       -xdropbelow [value]
           Specify xdrop cutoff score (argument 0 means undefined). If undefined an optimal value
           is determined automatically depending on the error rate

       -extendgreedy [value]
           Extend seed to both sides using greedy algorithm with trimming of waves, optional
           parameter specifies sensitivity (default: 97)

       -minidentity [value]
           Specify minimum identity of matches as integer in the range from 70 to 99 (for xdrop
           and greedy extension) (default: 80)

       -a [value]
           show alignments/sequences for exact matches (optional argument is number of columns
           per line) (default: 70)

       -ii [string]
           Specify input index (default: undefined)

       -scan [yes|no]
           scan index rather than map it to main memory (default: no)

       -v [yes|no]
           be verbose (default: no)

       -help
           display help and exit

       -version
           display version information and exit

REPORTING BUGS

       Report bugs to <kurtz@zbh.uni-hamburg.de>.