Welcome to the nanoCEM's documentation !

nanoCEM (nanopore Current Events Magnifier)

A Python command-line tool designed to visualize and analyse multiple statistical features of current events from nanopore sequencing data.

Installation

Before pip install, make sure you have installed the samtools(>=1.16) , f5c(>=1.4), slow5tools(>=1.1.0), minimap2(>=2.17), and python (>=3.7,<=3.10)

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

Content

• Quick start
• Output files description
• Data preparation from raw reads
• Command line arguments
• Description of statistical features
• Adaption for preprocessing methods
• An example for application
• Contacts