Installation

Spl-IsoQuant requires a 64-bit Linux system or Mac OS and Python (3.8 and higher) to be pre-installed on it. Note that Spl-IsoQuant 2.2.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)

Installing from GitHub

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

git clone https://github.com/algbio/spl-IsoQuant.git
cd spl-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 Spl-IsoQuant installation run

splisoquant.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:

=== Spl-IsoQuant pipeline finished ===
=== TEST PASSED CORRECTLY ===