GT-SEQ(1)

✨ NAME ✨

okay so bestie, gather round 💖 this is gt-seq — it's part of the GenomeTools manual (section 1, the user commands, yk). what it does is: parse the sequence file(s) you hand it and construct the corresponding index files. that's the whole vibe. indexing. slay. 🎀

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🌸 SYNOPSIS 🌸

gt seq [option ...] sequence_file [...]

so like, gt seq, then however many options you want, then one or more sequence files. easy. periodt. 💅

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💖 DESCRIPTION 💖

here's every single option, no skips, no cap. read them all, bestie, they're iconic:

• -recreate [yes|no] — recreate the index files even if they already exist. like, yes we know they're there, we're doing it anyway. (default: no)
• -showfasta [yes|no] — show all the sequences, in FASTA format. (default: no)
• -showseqnum [value] — show the sequence with the given number. heads up: sequences are counted from 1 unless -seqnum_from_0 is specified. (default: undefined)
• -showseqlength [value] — show the length of the sequence with the given number. again: counted from 1 unless -seqnum_from_0 is specified. (default: undefined)
• -showseqnum_inputfile [filename] — show the sequences with the given numbers, specified line by line in the given file. and yes, same deal: counted from 1 unless -seqnum_from_0 is specified. (default: undefined)
• -seqnum_from_0 [yes|no] — for the options -showseqnum and -showseqnum_inputfile: count sequence numbers from 0 instead of 1. (default: no)
• -gc-content [yes|no] — print the GC-content (for DNA files, bestie 🧬). (default: no)
• -stat [yes|no] — show sequence statistics. (default: no)
• -seqlengthdistri [yes|no] — show the sequence length distribution. (default: no)
• -width [value] — set the output width for FASTA sequence printing (a value of 0 disables formatting entirely). (default: 0)
• -o [filename] — redirect output to the specified file. (default: undefined)
• -gzip [yes|no] — write a gzip compressed output file. (default: no)
• -bzip2 [yes|no] — write a bzip2 compressed output file. (default: no)
• -force [yes|no] — force writing to the output file. (default: no)
• -help — display help and exit. 🫶
• -version — display version information and exit. ⭐

fr fr, don't sleep on those defaults — they're doing a lot of quiet work in the background. main character energy from the *no*s. 👑

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🦋 REPORTING BUGS 🦋

found a bug? not the vibe, but okay, tell the devs:

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

they'll handle it. go off. 💜

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okay and finally, the lil' sign-off — this whole thing is GenomeTools 1.6.6, dated 11/09/2025, and it lives in the manual as GT-SEQ(1). mwah. 🎀✨ bye bestie, go index something gorgeous 💖