{"repo":"zavolanlab/zarp","free":true,"listed":false,"github":"https://github.com/zavolanlab/zarp","clone":"git clone https://github.com/zavolanlab/zarp.git","description":"The Zavolab Automated RNA-seq Pipeline","language":"Python","stars":36,"topics":["bioinformatics","rna-seq","snakemake","conda","docker","fair","high-throughput","pipeline","reproducible-research","singularity"],"license":"Apache-2.0","category":"deployment-docker-iac","readme_excerpt":"ZARP ([Zavolab][zavolan-lab] Automated RNA-seq Pipeline) 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][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 ! Documentation For the full documentation please visit the ZARP website. Quick installation IMPORTANT: Rather than installing the ZARP workflow as described in this section, we recommend installing ZARP-cli for most use cases! If you follow its installation instructions, you can skip the instructions below. Quick installation requires the following: - Linux - Git - [Conda][conda] = 24.11.3 - Optional: [Apptainer][apptainer] =1.3.6 (required only if you want to use conta","default_branch":null,"files":null,"tree":[],"storefront":"/r/zavolanlab","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/zavolanlab/zarp/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}