AbSplice 2

AbSplice 2 is a method that predicts aberrant splicing across human tissues and developmental stages, as described in Wagner, Çelik et al., Nature Genetics 2023, Wagner et al., biorxiv 2025.

How to use AbSplice 2

Installation with container

Instead of Docker you can also use Podman (you just need to replace docker with podman in all the commands).

Download the image archive (file size is 2.2GB):

wget https://zenodo.org/record/16567295/files/absplice2.oci.tar

Load the image from archive:

docker load -i absplice2.oci.tar

Run the image with command line interface:

docker run -it --name absplice2_container localhost/absplice2_docker:latest /bin/bash

Now you are working inside the container. The conda environment is already installed here, you just need to activate it:

conda activate absplice_dock

Clone the AbSplice repository to the container:

git clone https://github.com/gagneurlab/absplice2.git
cd absplice2

Install the AbSplice package:

pip install -e .

Installation with creating a conda environment

Clone git repo:

git clone https://github.com/gagneurlab/absplice2.git

cd into repo directory:

cd absplice2

Note: users who already have the AbSplice 1 environment installed can skip the steps below and continue from Install modules from absplice

Install conda environment:

# Recommended if you have mamba installed
mamba env create -f environment.yaml
# otherwise
conda env create -f environment.yaml

Activate conda environment:

conda activate absplice

Install modules from absplice:

pip install -e .

If you want to reuse your AbSplice 1 environment, you also need to install the updated splicemap package:

pip install git+https://github.com/gagneurlab/splicemap.git@dev

Example use case

The example folder contains a snakemake workflow to generate AbSplice predictions, given a vcf file and a fasta file (either for hg19 or hg38, will be downloaded automatically).
The snakemake workflow will download precomputed SpliceMaps from Zenodo and run AbSplice based on these annotations. To generate predictions run:

cd example/workflow
python -m snakemake -j 1 --use-conda

AbSplice-DNA:

To run the workflow on your own data do the following:

• Store all (or provide a symlink to) vcf files for analysis in data/resources/analysis_files/vcf_files/.

• Specify the genome version that you are going to use (hg19 or hg38) in the field genome of the config file.

• In the field splicemap_tissues of the config file you can uncomment the tissues that AbSplice will use to generate predictions.

• NEW! If you want to generate developmental predictions, set the field devAbSplice to True and uncomment the desired tissues and timepoints in the fields dev_splicemap_tissues and dev_splicemap_timepoints of the config file.

For users who work with the container:

To run AbSplice on your own vcf-files, you need to copy them from your disk to the container. If you are inside the container, run:

exit

To copy a vcf-file from your disk to the container run:

docker cp path/on/your/disk absplice2_container:/app/absplice2/example/data/resources/analysis_files/vcf_files/

To execute the container run:

docker start absplice2_container
docker exec -it absplice2_container /bin/bash

To edit the config file inside the container use pre-installed editor nano as follows (or optionally install any other editor):

nano config.yaml

To close the editor press Ctrl+X, choose whether to save the changes: Y or N, and press Enter.