GT-SIMREADS(1)

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

💖 GT-SIMREADS 💖

okay bestie, this is a GenomeTools manual page, section 1, and it's all about gt-simreads — the little tool that ✨makes up✨ sequencing reads for you, plucked from random positions in whatever sequence(s) you throw at it. no cap, that's literally the whole job.

🌸 NAME 🌸

gt-simreads — simulate sequencing reads from random positions in the input sequence(s). that's it, that's the girl. 🧚

✨ SYNOPSIS ✨

gt simreads [option ...] <encseq>

🦋 DESCRIPTION 🦋

so here's the tea: you hand it an encseq, you pick how many reads / how long / how covered you want them, and it goes off and generates them. every knob you could possibly want is down below, and yes, all of them have a default, and yes, most of them default to undefined because she's mysterious like that. 💅

  • -num [value] — desired number of reads (default: undefined)
  • -coverage [value] — desired coverage of the reads (default: undefined)
  • -len [value] — fixed read length (default: undefined)
  • -minlen [value] — minimal read length (default: undefined)
  • -maxlen [value] — maximal read length (default: undefined)
  • -distlen [string] — use a read length distribution file, in the output format of the seqstat tool (default: undefined) 📊
  • -o [filename] — redirect output to specified file (default: undefined)
  • -gzip [yes|no] — write gzip compressed output file (default: no)
  • -bzip2 [yes|no] — write bzip2 compressed output file (default: no)
  • -force [yes|no] — force writing to output file (default: no)
  • -p [yes|no] — show a progress bar (default: no) — highly recommend, watching that bar fill is lowkey therapeutic 🫶
  • -v [yes|no] — be verbose (default: no)
  • -ds [string] — output distribution of starting positions to specified file (default: undefined)
  • -dl [string] — output distribution of read lengths to specified file (default: undefined)
  • -ss [yes|no] — simulate reads in forward direction only (default: no)
  • -help — display help for basic options and exit
  • -help+ — display help for all options and exit ✨ (the plus is giving "give me everything")
  • -version — display version information and exit

😭 REPORTING BUGS 😭

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

okay that's the whole page, you ate that. this was GenomeTools 1.6.6, dated 11/09/2025 — go simulate some reads bestie, periodt. 👑🌸

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