GT-ENCSEQ-CHECK(1)

💖 GT-ENCSEQ-CHECK(1) — the GenomeTools Manual, bestie edition 💖

okay so you know how there's a whole manual for GenomeTools? yeah, this page right here is the <pink>gt-encseq-check</pink> one, and it's genuinely one of my faves because it's short and it does exactly one job. we're gonna go through it together, no stress. 🫶

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✨ NAME ✨

gt-encseq-check — check the consistency of an encoded sequence file. that's it. that's the whole gig. it looks at your encseq and goes "hmm, is this actually coherent?" and tells you. iconic behaviour honestly. 💅

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🌸 SYNOPSIS 🌸

so you run `gt` with the subcommands `encseq check`, you optionally throw in some `option`s (there's a whole list below, we'll get there), and then you optionally hand it a `file`. that's the whole invocation. slay.

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# 🦋 DESCRIPTION 🦋

okay so this is where all the options live. ngl this section is literally just the flag list, so let's go through them one by one like we're doing a little unboxing video. ✨

- **`-scantrials`** *`[value]`* — here you get to specify the number of scan trials. the default is `0`, so if you don't say anything, it just... doesn't do that many. zero of them, actually. 🙈
- **`-multicharcmptrials`** *`[value]`* — specify the number of multicharacter trials. default is `0` again. same energy as above but for multicharacter stuff. 🍓
- **`-prefixlength`** *`[value]`* — sets the prefix length. default: `0`. just a lil number, no drama.
- **`-nocheckunit`** *`[yes|no]`* — do <red>not</red> run `checkextractunitatpos`. default is `no`, which lowkey means "no, don't skip it, go ahead and run it". yes/no semantics are like that sometimes, iykyk. 💀
- **`-mirrored`** *`[yes|no]`* — use a mirrored encseq. default is `no`. so by default you're getting the non-mirrored one, bestie. 🌈
- **`-v`** *`[yes|no]`* — be verbose. default is `no`. flip this to `yes` if you want it to actually *talk* to you instead of sitting there in silence. main character energy. 👑
- **`-help`** — display help and exit. the classic. always there for you. 🎀
- **`-version`** — display version information and exit. also the classic. also always there for you. ⭐

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# 😭 REPORTING BUGS 😭

found a bug? do NOT suffer in silence, bestie. take it straight to:

`https://github.com/genometools/genometools/issues`

they wanna hear about it, fr fr. that's literally what that page is for. 🔥

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<purple>and that's the whole page!! ty for reading, you ate that. this was **GenomeTools 1.6.6**, dated **11/09/2025**, and it's the `<pink>GT-ENCSEQ-CHECK(1)</pink>` page from the GenomeTools Manual. go check your encseqs, they deserve it. mwah 💜✨</purple>