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PROGRAM:

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)

-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>.

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