SYNOPSIS
gt seed_extend [option ...] encseq_basename [encseq_basename]
DESCRIPTION
-ii [string]
- Input index for encseq encoded sequences
-qii [string]
- Query input index (encseq)
-seedlength [value]
- Minimum length of a seed default: logarithm of input length to the basis alphabet size
-diagbandwidth [value]
- Logarithm of diagonal band width (for filter) (default: 6)
-mincoverage [value]
- Minimum coverage in two neighbouring diagonal bands (for filter) default: 2.5 x seedlength
-maxfreq [value]
- Maximum frequency of a k-mer (for filter) (default: undefined)
-memlimit [string]
- Maximum memory usage to determine the maximum frequency of a k-mer (for filter) (default: undefined)
-extendxdrop [value]
- Extend seed to both sides using xdrop algorithm, /noptional parameter specifies sensitivity (default: 97)
-xdropbelow [value]
- Specify xdrop cutoff score (0 means automatically defined depending on minidentity)
-extendgreedy [value]
- Extend seed to both sides using greedy algorithm, optional parameter specifies sensitivity (default: 97)
-l [value]
- Minimum alignment length (for seed extension) (default: undefined)
-minidentity [value]
- Minimum identity of matches (for seed extension) (default: 80)
-a [value]
- show alignments/sequences (optional argument is number of columns per line) (default: 70)
-no-reverse [yes|no]
- do not compute matches on reverse complemented strand (default: no)
-no-forward [yes|no]
- do not compute matches on forward strand (default: no)
-v [yes|no]
- be verbose (default: no)
-help
- display help and exit
-version
- display version information and exit