GT-READJOINER-PREF(1)

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

💖 GT-READJOINER-PREF(1) 💖

okay bestie, this is a page from the GenomeTools Manual and it's literally about gt-readjoiner-prefilter — the lil tool that yeets contained and low-quality reads out of your read set and then encodes what's left into GtEncseq format. iconic behavior honestly 🦋

✨ NAME ✨

gt-readjoiner-prefilter — Remove contained and low-quality reads and encode read set in GtEncseq format.

like. it cleans your reads AND packs them up cute. multitasking queen 👑

🌸 SYNOPSIS 🌸

gt readjoiner prefilter [option ...]

🎀 DESCRIPTION 🎀

So here's the whole menu of options, no cap, every single one:

  • -readset [string] — tells it what to call the readset. default is literally just the filename of the first input sequence_file, slay.
  • -db — hands it a list of input libraries (Fasta/FastQ). the way you write this depends on your setup, so listen up:
    • for single-end libraries: just use the filename. but heads up — that filename is not allowed to contain : symbols. periodt.
    • for paired-end libraries where the reads are interleaved (f,r,f,r,...) all in one single file: use the notation <filename>:<insertlength>[,<stdev>] (the <stdev> part can be omitted, no pressure).
    • for paired-end where the reads live in two separate files (f, r): use the notation <file_f>:<file_r>:<insertlength>[,<stdev>].
  • -v [yes|no] — be verbose. (default: no) like, do you want it to talk to you? 🙈
  • -q [yes|no] — suppress standard output messages. (default: no) shhh era 🤫
  • -des [yes|no] — store Fasta IDs (or entire descriptions if used together with -clipdes no). ⚠️ warning: increases the memory requirement. (default: no)
fr fr, watch your RAM on this one, she eats.
  • -clipdes [yes|no] — clip Fasta descriptions after first space. set it to false if you need the entire descriptions. (default: yes)
  • -memdes [yes|no] — use memory storage for descriptions. (default: use temporary disk storage) so by default it's being polite and using your disk 🫶
  • -maxlow [value] — the maximal number of low-quality positions a read can have. default: infinite. so by default, nothing gets flagged as too-low-quality. zero gatekeeping ✨
  • -lowqual [value] — the maximal quality for a position to even be considered low-quality. (default: 3)
  • -phred64 [yes|no] — use phred64 scores for FastQ format. (default: no)
  • -help — display help for basic options and exit. short and sweet 💅
  • -help+ — display help for all options and exit. the deluxe version 👑
  • -version — display version information and exit.

💀 REPORTING BUGS 💀

Found a bug? not the vibe. report it here:

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

and that's the whole thing bestie, you ate 🍓

GenomeTools 1.6.6 — 11/09/2025 — mwah, catch you on the next page 💖🦋✨

📦 where this page comes from