splicekit 0.8.2

splicekit: an integrative toolkit for splicing analysis from short-read RNA-seq

splicekit is a modular platform for splicing analysis from short-read RNA-seq datasets. The platform also integrates an JBrowse2 instance, pybio for genomic operations and scanRBP for RNA-protein binding studies. The whole analysis is self-contained (one single folder) and the platform is written in Python, in a modular way.

Check a short video presentation about splicekit (poster) at ECCB 2023 on Youtube:

Quick start

Since version 0.7, splicekit is a Snakemake pipeline, and there is also a Conda environment yaml file.

git clone git@github.com:bedapub/splicekit.git    # clone rep
cd splicekit                                      # change working directory

micromamba -y create -f splicekit.yaml            # create conda env
micromamba activate splicekit                     # activate env
./install.sh                                      # install dependencies
pip install .                                     # install splicekit

cd datasets/GSE126543                             # move to sample folder
./1_download.sh                                   # download sample FASTQs
pybio homo_sapiens                                # human genome

./run_snakemake_local.sh --configfile config.yaml # run snakemake (local)
./run_snakemake_slurm.sh --configfile config.yaml # OR run snakemake SLURM

After snakemake finishes, you can explore results interactively running splicekit web and follow instructions on how to open the html reports in your browser.

pip install git+https://github.com/bedapub/splicekit.git@main

Documentation

• PDF reference manual
• Google docs of the above PDF (comment if you like)

Changelog

v0.8.1: released in July 2026

• added bam_file column support in samples.tab for per-sample BAM paths (subfolder layouts)
• new get_bam_path(sample_id) helper in splicekit/core/annotation.py — falls back to {bam_path}/{sample_id}.bam when no per-sample path is given
• exons.py, genes.py, anchors.py: replaced os.listdir() BAM discovery with annotation.samples list + get_bam_path() (enables subfolder BAMs, no dir scan needed)
• junctions.py, jbrowse2.py: same get_bam_path() adoption
• default bam_column = "bam_file" added to config

v0.8: released in October 2025

• removed platform config option (now snakemake submits jobs to the cluster)
• pandas and other minor improvements

v0.7: released in February 2025

• Snakemake version
• Conda splicekit.yaml for environment setup

Citing and Contact

If you find splicekit useful in your work and research, please cite:

Rot, G., Wehling, A., Schmucki, R., Berntenis, N., Zhang, J. D., & Ebeling, M. (2024)
splicekit : an integrative toolkit for splicing analysis from short-read RNA-seq
Bioinformatics Advances, 4(1). https://doi.org/10.1093/bioadv/vbae121

In case of questions, issues and other ideas, please use the GitHub Issues or write directly to Gregor Rot.