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>.