Tombo

Introduction

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.

For more information, please check its website: https://biocontainers.pro/tools/ont-tombo and its home page on Github.

Versions

1.5.1

Commands

tombo

Module

You can load the modules by:

module load biocontainers
module load tombo

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Tombo on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=tombo
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers tombo

tombo resquiggle path/to/fast5s/ genome.fasta --processes 4 --num-most-common-errors 5
tombo detect_modifications alternative_model --fast5-basedirs path/to/fast5s/ \
    --statistics-file-basename native.e_coli_sample \
    --alternate-bases dam dcm --processes 4

# plot raw signal at most significant dcm locations
tombo plot most_significant --fast5-basedirs path/to/fast5s/ \
    --statistics-filename native.e_coli_sample.dcm.tombo.stats \
    --plot-standard-model --plot-alternate-model dcm \
    --pdf-filename sample.most_significant_dcm_sites.pdf

# produces wig file with estimated fraction of modified reads at each valid reference site
tombo text_output browser_files --statistics-filename native.e_coli_sample.dam.tombo.stats \
     --file-types dampened_fraction --browser-file-basename native.e_coli_sample.dam
# also produce successfully processed reads coverage file for reference
tombo text_output browser_files --fast5-basedirs path/to/fast5s/ \
    --file-types coverage --browser-file-basename native.e_coli_sample