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 with alphabet size as
           log-base

       -spacedseed [value]
           use spaced seed of length specified by option -seedlength (optional argument specifies
           weight of spaced seed) (default: 0)

       -diagbandwidth [value]
           Logarithm of diagonal band width in the range from 0 to 10 (for filter) (default: 6)

       -mincoverage [value]
           Minimum coverage in two neighbouring diagonal bands (for filter) default: 2.5 x
           seedlength

       -diagband-stat [...]
           Compute statistics from diagonal band scores; parameter specifies kind of statistics,
           possible choices are sum (default: sum)

       -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, optional 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)

       -maxmat [value]
           compute maximal matches of minimum length specified by option -l (default: 1)

       -l [value]
           Minimum length of aligned sequences (default: undefined)

       -minidentity [value]
           Minimum identity of matches (for seed extension) (default: 80)

       -evalue [value]
           switch on evalue filtering of matches (optional argument specifies evalue threshold)
           (default: 10.000000)

       -outfmt
           specify what information about the matches to display alignment: show alignment
           (possibly followed by =<number> to specify width of alignment columns, default is )
           seed_in_algn: mark the seed in alignment polinfo: add polishing information for shown
           alignment seed: abbreviation for seed.len seed.s seed.q failed_seed: show the
           coordinates of a seed extension, which does not satisfy the filter conditions
           fstperquery: output only the first found match per query tabsep: separate columns by
           tabulator, instead of space as default blast: output matches in blast format 7
           (tabular with comment lines; instead of gap opens, indels are displayed) gfa2: output
           matches in gfa2 format custom: output matches in custom format, i.e. no columns are
           pre-defined; all columns have to be specified by the user cigar: display cigar string
           representing alignment (no distinction between match and mismatch) cigarX: display
           cigar string representing alignment (distinction between match (=) and mismatch (X))
           trace: display trace, i.e. a compact representation of an alignment (possibly followed
           by =<delta>) to specify the delta-value; default value of delta is 50 dtrace: display
           trace as differences; like trace, but instead of an absolute value x, report the
           difference delta-x. This leads to smaller numbers and thus a more compact
           representation s.len: display length of match on subject sequence s.seqnum: display
           sequence number of subject sequence subject id: display sequence description of
           subject sequence s.start: display start position of match on subject sequence s.end:
           display end position of match on subject sequence strand: display strand of match
           using symbols F (forward) and P (reverse complement) q.len: display length of match on
           query sequence q.seqnum: display sequence number of query sequence query id: display
           sequence description of query sequence q.start: display start position of match on
           query sequence q.end: display end position of match on query sequence alignment
           length: display length of alignment mismatches: display number of mismatches in
           alignment indels: display number of indels in alignment gap opens: display number of
           indels in alignment score: display score of match editdist: display unit edit distance
           identity: display percent identity of match seed.len: display length seed of the match
           seed.s: display start position of seed in subject seed.q: display start position of
           seed in query s.seqlen: display length of subject sequence in which match occurs
           q.seqlen: display length of query sequence in which match occurs evalue: display
           evalue bit score: display bit score

       -ani [yes|no]
           output average nucleotide identity determined from the computed matches (which are not
           output) (default: no)

       -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)

       -use-apos [yes|no]
           Discard a seed only if both apos and bpos overlap with a previous successful alignment
           (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 https://github.com/genometools/genometools/issues.