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Installation

1. Creat anaconda environment

conda create -n tombo_env python=3.7

2. Set up channels

(https://bioconda.github.io/user/install.html#install-conda)

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

3. Install Tombo

conda install -c bioconda ont-tombo

4. Install ont_fast5_api

Install ont_fast5_api (https://pypi.org/project/ont-fast5-api/) for multi_to_single_fast5

pip install ont-fast5-api

5. Update NumPy

In Tombo, the version of NumPy must be lower 1.20，otherwise it will have ValueError: cannot convert float NaN to integer.(nanoporetech/tombo#319)

conda install numpy=1.19.5

Demo

Dataset: diaphragm_small.fast5

multi_to_single_fast5 --input_path multi_fast5/diaphragm_small.fast5  --save_path single_fast5_DNA --recursive -t 20
tombo resquiggle single_fast5_cDNA Mus_musculus.GRCm38.cdna.all.fa --overwrite --processes 10 --num-most-common-errors 0 --signal-matching-score 0
tombo plot genome_locations --fast5-basedirs single_fast5_cDNA/0 --genome-locations ENSMUST00000061618.8:3172