GT-SEQSTAT(1)

📦
version 1.6.6 · 5 versions
, in ubuntu resolute, ubuntu stonking

💅 GT-SEQSTAT — the vibe check your fasta files have been waiting for

okay so bestie, you know how you've got a pile of fasta files just sitting there and you're like "what even are you"? yeah. this is gt-seqstat, a tool from the GenomeTools manual that calculates statistics for your fasta file(s). it's giving lab notebook but make it cute. 🧬✨

🌸 SYNOPSIS 🌸

gt seqstat [options] file [...]

that's it. that's the whole summoning ritual. drop in your options, drop in your files, and let the girlies do the math. 💖

🎀 DESCRIPTION 🎀

this is where we get into the actual options, and ngl there are a few, but they're all iconic in their own way. every single one is listed below because we do not skip details in this house. periodt. 👑

  • -v [yes|no] — be verbose. default: no. so if you want her to actually talk to you, say yes.
  • -distlen [yes|no] — show distribution of sequence length. default: no. this is the one where you find out if your sequences are all over the place. 🦋
  • -b [value] — bucket size for the distlen option. default: 100. think of it as how chunky you want your histogram slices. 🍓
  • -binary [yes|no] — use a binary format for distlen output output filename: <first_input_filename>.distlen bucketsize: 1. default: no. (yes, the original really says "output output", i am simply reporting the facts, no cap. 😭) so the filename it spits out is literally <first_input_filename>.distlen and the bucketsize is 1.
  • -contigs [yes|no] — summary of contigs set statistics. default: yes. she's on by default because she's the main character. 💅
  • -nstats — list of N-values to calculate statistics for, terminated by --. if none given, N50 and N80 will be calculated. so like, you feed her your N-values and then close it off with --, and if you forget, she just does N50 and N80 for you. no stress. ✨
  • -astretch [yes|no] — show distribution of A-substrings. default: no. the As get their own little spotlight. 💜
  • -genome [value] — set genome length for NG50/NG80 calculation. default: 0. this is the number NG50/NG80 needs, so set it if you want those stats to actually mean something. 🔥
  • -help — display help for basic options and exit. the quick lil "what do i do" button. 🫶
  • -help+ — display help for all options and exit. the deluxe edition. the full tour. 👑
  • -version — display version information and exit. say hi, then dip. 🌈
ok real talk bestie: that -nstats list has to be terminated by --, and if you don't pass any N-values at all, N50 and N80 are what you get. and -binary writes to a file named after your first input file, so heads up on that. 🚨

😭 REPORTING BUGS 😭

found something cursed? report bugs to https://github.com/genometools/genometools/issues. the maintainers want to hear about it fr fr. 🙈

anyway that's the whole page, you're literally a sequence-statistics girlie now. go forth and gt seqstat your files. slay. 🎀

this was GenomeTools 1.6.6, dated 11/09/2025. bye bestie, love u, mwah 💖🦋✨

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