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