TOMBO(1)

📦 version 1.5.1, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 TOMBO(1) — the manual page, but make it make sense 💖

okay bestie, grab your boba because we're about to talk about tombo, a whole suite of tools for spotting modified nucleotides hiding in raw nanopore sequencing data. yes, that's the actual name, and yes, it's serving. 🦋

✨ NAME ✨

tombo — identification of modified nucleotides from raw nanopore sequencing data

🌸 SYNOPSIS 🌸

tombo [-h] [-v]
{resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot}
...

👑 DESCRIPTION 👑

Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data.

Tombo also provides tools for the analysis and visualization of raw nanopore signal. it's giving "one tool, two jobs, no complaints". 💅

Tombo command groups (additional help available within each command group):

  • resquiggle — Re-annotate raw signal with genomic alignment from existing basecalls. it's literally re-telling the story of your signal, but with receipts. 🔥
  • preprocess — Pre-process nanopore reads for Tombo processing.
  • filter — Apply filter to Tombo index file for specified criterion.
  • detect_modifications — Perform statistical testing to detect non-standard nucleotides. this is the main character of the whole operation, ngl. 👑
  • text_output — Output Tombo results in text files.
  • build_model — Create canonical and alternative base Tombo models.
  • plot — Save plots to visualize raw nanopore signal or testing results. aesthetic AND informative, we love to see it. 📊

🎀 OPTIONAL ARGUMENTS 🎀

  • -h, --help — show this help message and exit. when you're lost, bestie, just ask. 🫶
  • -v, --version — show Tombo version and exit. vibe check: what era of tombo are we in? ⭐

🙈 AUTHOR 🙈

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. iconic behavior, honestly. 🎀

no cap, everything above is exactly what the original page says — every command, every flag, every word. periodt. 💜

okay that's the whole page, bestie! this doc is from tombo 1.5.1, dated June 2020 — a little vintage, lowkey timeless. go forth and detect some modifications. 🦋✨

📦 where this page comes from