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gt-tagerator - Map short sequence tags in given index.


gt tagerator [options] -q tagfile [-esa|-pck] indexname


Specify files containing the short sequence tags

-e [value]
Specify the allowed number of differences (replacements/insertions/deletions)

-esa [string]
Specify index (enhanced suffix array) (default: undefined)

-pck [string]
Specify index (packed index) (default: undefined)

-nod [yes|no]
Do not compute direct matches (default: no)

-nop [yes|no]
Do not compute palindromic matches (i.e. no reverse complemented matches.) (default:

-best [yes|no]
Compute only best matches, i.e. only for smallest edit distance with matches (default:

-maxocc [value]
specify max number of match-occurrences (default: 0)

-skpp [yes|no]
Skip prefix of pattern (only in pdiff mode) (default: no)

-withwildcards [yes|no]
output matches containing wildcard characters (e.g. N); only relevant for approximate
matching (default: yes)

use combination of the following keywords to specify output tagnum show ordinal number
of tag tagseq show tag sequence dblength show length of match in database dbstartpos
show start position of match in database abspos show absolute value of dbstartpos
dbsequence show sequence of match strand show strand edist show edit distance
tagstartpos show start position of match in tag (only for -maxocc) taglength show
length of match in tag (only for -maxocc) tagsuffixseq show suffix tag involved in
match (only for -maxocc)

-v [yes|no]
be verbose (default: no)

display help and exit

display version information and exit


Report bugs to <kurtz@zbh.uni-hamburg.de>.

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