GT-TAGERATOR(1)

✨ GT-TAGERATOR 💅

okay bestie, so this is gt-tagerator, part of the GenomeTools manual (section 1, the "just run me in a terminal" section 🫶). It maps short sequence tags into a given index. Yes it's giving bioinformatics. Yes it's iconic. Let's go 💖

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✨ NAME ✨

gt-tagerator — map short sequence tags in given index 🧚

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✨ SYNOPSIS ✨

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

like... you give it a tagfile with -q, you pick an index flavour with -esa or -pck, and then you name the indexname. that's the whole vibe. 🌸

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✨ DESCRIPTION ✨

every flag, every default, no skips, no cap 💅

• -q — specify files containing the short sequence tags. this is the tagfile, the main character of the operation 👑
• -e [value] — specify the allowed number of differences (replacements/insertions/deletions). so like, how much sloppiness you're willing to forgive in a match 😭
• -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: no.
• -best [yes|no] — compute only best matches, i.e. only for smallest edit distance with matches. default: no. this one's for when you only want the top-tier, no crumbs 🎀
• -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.
• -output — use a 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)

fr fr, stack them however you want — it's a combo, not a single pick 🍓

• -v [yes|no] — be verbose. default: no. turn this on when you want the program to tell you everything it's doing, like a bestie recapping drama 🌈
• -help — display help and exit.
• -version — display version information and exit.

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✨ REPORTING BUGS ✨

found something cursed? report bugs to <kurtz@zbh.uni-hamburg.de>. be nice, be specific, include the receipts 🫶

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and that's the page!! this was GenomeTools 1.6.6, dated 11/09/2025 💖 go map those tags bestie, you're literally built for this 💅✨🦋