Installation

IsoQuant requires a 64-bit Linux system or Mac OS and Python (3.8 and higher) to be pre-installed on it. Note that IsoQuant 3.11.x and earlier versions are not well compatible with Python 3.14. No special hardware is required.

You will also need

• gffutils
• pysam
• pyfaidx
• ssw-py
• editdistance
• biopython
• numba
• minimap2
• samtools
• STAR (optional)

and some other common Python libraries. The full requirements list can be found in requirements.txt.

Installing from conda

IsoQuant can be installed with conda:

conda create -c conda-forge -c bioconda -n isoquant python=3.12 isoquant

Typically, conda installation takes a few minutes.

Installing from GitHub

To obtain IsoQuant you can download the repository and install the requirements.
Clone IsoQuant repository and switch to the latest release:

git clone https://github.com/ablab/IsoQuant.git
cd IsoQuant
git checkout latest

Install requirements:

pip install -r requirements.txt

Typically, package installation takes a few minutes.

You also need samtools and minimap2 to be in the $PATH variable.

Verifying your installation

To verify IsoQuant installation run

isoquant.py --test

to run on toy dataset. This should typically take less than 1 minute.

If the installation is successful, you will find the following information at the end of the log:

=== IsoQuant pipeline finished ===
=== TEST PASSED CORRECTLY ===