GT-READJOINER-ASSE(1)

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

💖 GT-READJOINER-ASSEMBLY 💖

okay so bestie, welcome to the manual page for gt-readjoiner-assembly from the GenomeTools manual (page GT-READJOINER-ASSE(1)). sit down, grab a strawberry 🍓, and let's get into it, because this one is actually kinda iconic.

✨ NAME ✨

gt-readjoiner-assembly — construct string graph and output contigs. that's it, that's the whole job, and it ate. 👑

✨ SYNOPSIS ✨

gt readjoiner assembly [option ...]

✨ DESCRIPTION ✨

so like, this is where all the options live. every single one of them. no skips, no skimming, we're doing the full tour 💅

  • -readset [string] — specify the readset name (default: undefined). yeah, undefined, she starts out nameless fr.
  • -spmfiles [value] — number of SPM files to read. heads up bestie: this must be equal to the value of -j for the overlap phase (default: 1).
  • -l [value] — specify the minimum SPM length (default: 0).
  • -depthcutoff [value] — specify the minimal number of nodes in a contig (default: 3).
  • -lengthcutoff [value] — specify the minimal length of a contig (default: 100).
  • -errors [yes|no] — search graph features which may originate from sequencing errors and remove them (default: no).
  • -bubble [value] — number of rounds of p-bubble removal to perform (default: 3).
  • -deadend [value] — number of rounds of dead end removal to perform a dead end (default: 10).
  • -deadend-depth [value] — specify the maximal depth of a path to an end-vertex by which the path shall be considered a dead end (default: 10).
  • -v [yes|no] — be verbose (default: no). she's chatty when you let her be 🗣️
  • -q [yes|no] — suppress standard output messages (default: no). the "not me talking" setting, lowkey.
  • -help — display help for basic options and exit.
  • -help+ — display help for all options and exit. the plus sign is doing the most and I respect it ✨
  • -version — display version information and exit.

✨ REPORTING BUGS ✨

Report bugs to https://github.com/genometools/genometools/issues.

not me asking you to file an issue, but like… if something's broken, tell the devs, they're nice I promise 🫶

and that's the whole page, bestie! this was GenomeTools 1.6.6, dated 11/09/2025, and honestly? iconic behavior. go build some contigs. periodt. 💖🦋🎀

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