Metadata-Version: 2.1
Name: nanoCEM
Version: 0.0.3.2
Summary: A simple tool designed to visualize the features that distinguish between two groups of ONT data at the site level.                It supports two re-squiggle program(tombo and f5c).
Home-page: https://github.com/lrslab/nanoCEM
Author: GUO Zhihao
Author-email: qhuozhihao@icloud.com
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7,<3.10
Description-Content-Type: text/markdown
License-File: LICENSE

# nanoCEM ![logo](docs/logo_tiny.png "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](https://github.com/hiruna72/squigualiser) is recommended.

## Installation

Before pip installation, make sure you had installed the `samtools`(>=1.16) and `minimap2`(>=2.17),

    conda install -c bioconda samtools minimap2

To install the latest nanoCEM

    pip install nanoCEM

See our Installation page for details. 

To check the version of nanoCEM, run:

    pip list | grep nanoCEM


 **Notes:** Additionally, we do not rely on any re-squiggle or eventalign packages. We only need their index files for the sequencing data.


## Data release
For the data we used and related commands in our paper, please view our [wiki](https://github.com/lrslab/nanoCEM/wiki/Data-release-and-commands)

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