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GT-REPFIND(1) GenomeTools Manual GT-REPFIND(1)

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>.
07/29/2016 GenomeTools 1.5.9