GenomeTools - manual page for 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>.