GT-ENCSEQ-ENCODE(1)

🌸 GT-ENCSEQ-ENCODE 🌸

bestie. okay. so this is gt-encseq-encode, and it's sitting in section 1 of the GenomeTools Manual. it's the tool that encodes your sequence files so they take up way less room, and honestly? she's iconic for it. 💅

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✨ NAME ✨

gt-encseq-encode — encodes sequence files (FASTA/FASTQ, GenBank, EMBL) efficiently. that last word is doing a LOT of heavy lifting and she knows it. 👑

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✨ SYNOPSIS ✨

gt encseq encode sequence_file [sequence_file [sequence_file ...]]

so you just throw one file at her. or two. or like, as many as your little heart desires, no cap. 🫶

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✨ DESCRIPTION ✨

here's the whole menu of flags, bestie. read them. love them. don't skip any of them because every single one matters. 🎀

• -showstats [yes|no] — show the compression results, like a little before/after glow-up report (default: no)
• -ssp [yes|no] — write the sequence separator positions out to a file (default: yes)
• -des [yes|no] — write the sequence descriptions out to a file (default: yes)
• -sds [yes|no] — write the sequence description separator positions out to a file (default: yes)
• -md5 [yes|no] — write MD5 sums out to a file (default: yes)
• -clipdesc [yes|no] — clip descriptions after the first whitespace (default: no)
• -sat [string] — tell her what kind of sequence representation to use, by picking exactly one of these keywords: direct, bytecompress, eqlen, bit, uchar, ushort, uint32 (default: undefined)
• -dna [yes|no] — the input is a DNA sequence (default: no)
• -protein [yes|no] — the input is a protein sequence (default: no)
• -plain [yes|no] — process it as plain text (default: no)
• -dust [yes|no] — mask the low-complexity regions using the dust algorithm (default: no)
• -dustwindow [value] — the windowsize for the dust algorithm (default: 64)
• -dustthreshold [value] — the threshold for the dust algorithm (default: 2.000000)
• -dustlink [value] — the max. distance between regions masked by dust before they get merged together (default: 1)
• -indexname [string] — give a name to the index that's gonna be generated (default: undefined)
• -smap [string] — point to the file that contains a symbol mapping (default: undefined)
• -lossless [yes|no] — allow lossless original sequence retrieval, so you can get the original back (default: no)
• -v [yes|no] — be verbose, aka spill the tea about everything she's doing (default: no)
• -help — display help for the basic options and then exit
• -help+ — display help for all the options and then exit (yes, the plus is doing the most, and she earned it)
• -version — display version information and then exit

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✨ REPORTING BUGS ✨

found a bug? don't suffer in silence, bestie, that's not the vibe. report it here:

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

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and that's the whole page!! 🦋 you understood all of it, i'm so proud, main character energy fr fr. 💖

this was GenomeTools 1.6.6, dated 11/09/2025 — mwah, slay, periodt. 💅✨