ZARP

Welcome to the ZARP documentation pages!

ZARP is a generic RNA-Seq analysis workflow that allows users to process and analyze Illumina short-read sequencing libraries with minimum effort. Better yet: With our companion ZARP-cli command line interface, you can start ZARP runs with the simplest and most intuitive commands.

RNA-seq analysis doesn't get simpler than that!

The workflow is developed in Snakemake, a widely used workflow management system in the bioinformatics community. ZARP will pre-process, align and quantify your single- or paired-end stranded bulk RNA-seq sequencing libraries with publicly available state-of-the-art bioinformatics tools. ZARP's browser-based rich reports and visualizations will give you meaningful initial insights in the quality and composition of your sequencing experiments - fast and simple. Whether you are an experimentalist struggling with large scale data analysis or an experienced bioinformatician, when there's RNA-seq data to analyze, just zarp 'em!

How does it work?

ZARP requires Conda or Mamba to install the basic dependencies. Each individual step of the workflow runs either in its own Apptainer (Singularity) container or in its own Conda virtual environment.

Once the installation is complete, you fill in a config.yaml file with parameters and a samples.tsv file with sample specific information. You can easily trigger ZARP by making a call to snakemake with the appropriate parameters.

The pipeline can be executed in different systems or High Performance Computing (HPC) clusters. ZARP generates multiple output files that help you Quality Control (QC) your data and proceed with downstream analyses. Apart from running the main ZARP workflow, you can also run a second pipeline that pulls sequencing sample data from the Sequence Read Archive (SRA), and a third pipeline that populates a file with the samples and infers missing metadata.

How to cite

If you use ZARP in your work, please kindly cite the following article:

ZARP: A user-friendly and versatile RNA-seq analysis workflow
Maria Katsantoni, Foivos Gypas, Christina J. Herrmann, Dominik Burri, Maciej Bak, Paula Iborra, Krish Agarwal, Meric Ataman, Máté Balajti, Noè Pozzan, Niels Schlusser, Youngbin Moon, Aleksei Mironov, Anastasiya Börsch, Mihaela Zavolan, Alexander Kanitz
F1000Research 2024, 13:533
https://doi.org/10.12688/f1000research.149237.1

Info materials

Poster

Reach out

There are several ways to get in touch with us:

• For ZARP usage questions, please use the ZARP Q&A forum (requires GitHub registration)
• For feature suggestions and bug reports, please use either the ZARP or ZARP-cli issue tracker (requires GitHub registration)
• For any other requests, please reach out to us via email

Contributors welcome!

Open source contributors are always welcome, for ZARP, ZARP-cli or any other of the Zavolab projects. Simply reach out by email to schedule an onboarding call.

Acknowledgements