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GT-SEED_EXTEND(1) GenomeTools Manual GT-SEED_EXTEND(1)

NAME

gt-seed_extend - Calculate local alignments using the seed and extend algorithm.

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)
-parts [value]
Divide data into specified number of parts (default: 1)
-kmerfile [yes|no]
Use pre-calculated k-mers from file (if exist) (default: yes)
-v [yes|no]
be verbose (default: no)
-help
display help and exit
-version
display version information and exit

REPORTING BUGS

Report bugs to <gt-users@genometools.org>.
07/29/2016 GenomeTools 1.5.9