MultiQC Overview
MultiQC is a powerful reporting tool that consolidates results and statistics from various bioinformatics outputs, including log files and console outputs. It effectively summarizes experiments that involve multiple samples and various analysis steps. This tool is intended to be utilized at the conclusion of analysis pipelines or can be executed manually once you have completed running your bioinformatics tools.
Installing MultiQC
To install MultiQC, the first requirement is Python. The simplest method to achieve this is by using Conda (refer to the full documentation).
Here’s a step-by-step guide:
1. If not already installed, Download Miniconda suitable for your operating system.
2. Run the installer application and follow the on-screen instructions.
3. Open your “Anaconda Prompt” terminal shell to run the following.
4. Configure your Conda channels to enable compatibility with Bioconda:
conda config –-add channels bioconda
conda config --add channels conda-forge
conda config -–set channel-priority strict
5. Create a new Conda environment:
conda create –-name myenv python=3.11
conda activate myenv
6. Install MultiQC on Conda Environment:
conda install multiqc
7. Check if it worked by writing the following in the terminal. For Teton analysis, the user should install a version greater than or equal to v1.29
multiqc --version
Additionally, there are several installation methods tailored to your usage needs and familiarity with the Python ecosystem.
If you're new to software packaging, the options may seem daunting. A helpful guideline is as follows:
- Running MultiQC in a pipeline? Use Docker or Singularity.
- Running MultiQC locally? Opt for Pip or Conda
Method | Command |
Pip | pip install multiqc |
Pip (dev version) | pip install --upgrade --force-reinstallgit+https://github.com/MultiQC/MultiQC.git |
Conda | conda install multiqc |
Docker | docker run -t -v `pwd`:`pwd` -w `pwd` multiqc/multiqc multiqc . |
Running MultiQC
Running MultiQC is quite straightforward. Simply direct it to the directory containing your run data, and it will automatically search recursively for any recognizable data.
If you are still in the directory where you extracted the data, the current working directory (.) contains your files. You can execute the following command:
multiqc .
Alternatively, you can also run MultiQC by specifying the input and output folder
multiqc /input_directory /output_directory