GT-COMPREADS-REFCO(1)

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

💖 GT-COMPREADS-REFCO 💖

okay bestie, so this is gt-compreads-refcompress from the GenomeTools Manual — it's the little tool that makes your fastq data smol with Reference Compressed Reads (RCR) ✨ like it's literally the glow-up your read files have been waiting for 🫶

✨ SYNOPSIS ✨

gt compreads refcompress [option ...] (-bam file -ref file)

so yeah, you run gt compreads refcompress, you throw some options at it, and you gotta give it -bam file and -ref file — those two are non-negotiable fr fr 💅

🎀 DESCRIPTION 🎀

here's the whole menu of options, no skips, no cuts, we're doing all of them:

  • -v [yes|no] — be verbose (default: no). aka let it yap and tell you what it's doing 💬
  • -mquals [yes|no] — store mapping quality for each read (default: no)
  • -quals [yes|no] — store all quality values for each read. heads up bestie, this implies enabling the option vquals (default: no)
  • -vquals [yes|no] — store quality values of read positions having variations compared to reference (default: no)
  • -descs [yes|no] — store read name for each read (default: no)
  • -ureads [yes|no] — store unmapped reads in a separated fastq file. the base name will be the value given in name and the suffix will be " _unmapped.fastq" (default: no). note the space in that suffix, don't come for me, it's literally in the manual 😭
  • -ref [string] — Index file (generated by the gt encseq tool) for reference genome. (default: undefined) 🧬
  • -bam [string] — File containing alignment of reads to genome (sorted ".bam" file). (default: undefined)
  • -name [string] — specify base name for RCR to be generated. if you don't set it, the base name will be set to the base name of the value you gave for the option bam (default: undefined) 👑
  • -help — display help and exit
  • -version — display version information and exit
lowkey important: -ref wants the index file made by gt encseq, not just any old genome file, and -bam wants a sorted .bam. iykyk 💀

🦋 REPORTING BUGS 🦋

found a bug? not the vibe, but okay — report it to https://github.com/genometools/genometools/issues and the maintainers will handle it 💜

that's the whole page bestie, you ate 🍓 this was GenomeTools 1.6.6, dated 11/09/2025 — go compress some reads, you main character 🧚✨

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