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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15.
.TH TOMBO "1" "June 2020" "tombo 1.5.1" "User Commands"
.SH NAME
tombo \- identification of modified nucleotides from raw nanopore sequencing data
.SH SYNOPSIS
.B tombo
[\-h] [\-v]
{resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot}
\&...
.SH DESCRIPTION
Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data.
.PP
Tombo also provides tools for the analysis and visualization of raw nanopore signal.
.SH "Tombo command groups (additional help available within each command group):"
.TP
resquiggle
Re\-annotate raw signal with genomic alignment from existing basecalls.
.TP
preprocess
Pre\-process nanopore reads for Tombo processing.
.TP
filter
Apply filter to Tombo index file for specified criterion.
.TP
detect_modifications
Perform statistical testing to detect non\-standard nucleotides.
.TP
text_output
Output Tombo results in text files.
.TP
build_model
Create canonical and alternative base Tombo models.
.TP
plot
Save plots to visualize raw nanopore signal or testing results.
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-v\fR, \fB\-\-version\fR
show Tombo version and exit.
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.
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