CGAT Apps

CGAT Apps is a collection of scripts to aid the analysis of high-throughput sequencing data.

After installation, use the cgat command to see how to use them.

Documentation

We are attempting to improve our documentation. However, our current documentation can be found here

For questions, please open a discussion on the GitHub issue page

Installation

Conda Installation

The preferred method to install CGAT Apps is using the installation script, which uses mamba, the fast C implementation of Conda.

To install cgat-apps using mamba::

mamba install -c conda-forge -c bioconda cgat-apps

Developers: try the installation script

Here are the steps::

    # Install conda and mamba according the the documentation. Next
    # install the conda packages for cgat-apps to work
    conda env create -f conda/environments/cgat-apps.yml

    # enable the conda environment
    conda activate cgat-a

    # Install the development version of cgat-apps
    python setup.py develop

    # finally, please run the cgat command-line tool to check the installation:
    cgat --help

The installation script will put everything under the specified location. The aim is to provide a portable installation that does not interfere with the existing software. As a result, you will get a conda environment working with CGAT Apps which can be enabled on demand according to your needs.

Usage

Run the cgat --help command to see what scripts are available and how to use them. For example, to strip sequence and quality information from a bam_ file, type::

cgat bam2bam --strip=sequence < in.bam > out.bam