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 via pip

Simply run:

pip install isoquant

Installing via conda

IsoQuant can be installed with conda using the bioconda channel:

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

Installing from GitHub

To get IsoQuant from GitHub, you can clone the repository:

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

Or download the latest release here.

IsoQuant can then be installed using pip:

pip install -e .

Alternatively, you can install the requirements manually:

pip install -r requirements.txt

Add samtools and minimap2 to the $PATH variable and run IsoQuant without intalling it.

Typically, the whole installation takes a few minutes regardless of the method.

Verifying your installation

To verify IsoQuant installation run

isoquant --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 ===