---
name: "tombo"
section: "1"
platform: "linux"
package: "tombo"
version: "1.5.1-7+b2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/tombo"
---

# tombo(1)

identification of modified nucleotides from raw nanopore sequencing data

## 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.

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

- resquiggle

  Re-annotate raw signal with genomic alignment from existing basecalls.

- 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.

- 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.

### optional arguments:

- **-h**, **--help**

  show this help message and exit

- **-v**, **--version**

  show Tombo version and exit.

## AUTHOR

 This manpage was written by Andreas Tille for the Debian distribution and\
  can be used for any other usage of the program.