nanoCEM

The nanopore current events magnifier (nanoCEM) is a python command line to facilitate the analysis of DNA/RNA modification sites by visualizing statistical features of current events. NanoCEM can be used to showcase high confidence sites and observe the difference based on the modification sample and the low or no modification sample.

It supports two re-squiggle pipeline(Tombo and f5c) and support R9 and R10. If you want to view single read signal or raw signal, Squigualiser is recommended.

Installation

Before pip install, make sure you have installed the samtools(>=1.16) , f5c(>=1.4), slow5tools(>=1.1.0) and minimap2(>=2.17),

conda install samtools=1.16 minimap2 f5c=1.4 slow5tools -c conda-forge -c bioconda 

To install the latest nanoCEM

pip install nanoCEM

And install from the resource

git clone https://github.com/lrslab/nanoCEM.git
cd nanoCEM/
pip install .

To install nanoCEM from docker,

docker pull zhihaguo/nanocem_env

To check the version of nanoCEM, run:

pip list | grep nanoCEM

Solutions for some potential environment problem

Although it does not affect the functionality, the issue of possible missing header files caused by samtools installation by conda can be resolved with the following command.

conda install -c conda-forge ncurses

The potential vbz format compression issue when reading fast5 files.

conda install -c bioconda ont_vbz_hdf_plugin

Data release

For the data we used and related commands in our paper, please view our wiki

Documents

Full documentation is available at https://nanocem.readthedocs.io/

Publication

Our paper is online here now

Workflow