table of contents
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>.01/06/2017 | GenomeTools 1.5.9 |