README.md

ZARP

Snakemake workflow that covers common steps of short read RNA-Seq library analysis developed by the Zavolan lab.

Reads are analyzed (pre-processed, aligned, quantified) with state-of-the-art tools to give meaningful initial insights into the quality and composition of an RNA-Seq library, reducing hands-on time for bioinformaticians and giving experimentalists the possibility to rapidly assess their data.

Below is a schematic representation of the individual steps of the workflow ("pe" refers to "paired-end"):

For a more detailed description of each step, please refer to the [workflow documentation][workflow-documentation].

Requirements

Currently the workflow is only available for Linux distributions. It was tested on the following distributions:

• CentOS 7.5
• Debian 10
• Ubuntu 16.04, 18.04

Installation

Cloning the repository

Traverse to the desired directory/folder on your file system, then clone/get the repository and move into the respective directory with:

git clone ssh://git@git.scicore.unibas.ch:2222/zavolan_group/pipelines/zarp.git
cd zarp

Installing Conda

Workflow dependencies can be conveniently installed with the Conda package manager. We recommend that you install Miniconda for your system (Linux). Be sure to select Python 3 option. The workflow was built and tested with miniconda 4.7.12. Other versions are not guaranteed to work as expected.

Installing dependencies

For improved reproducibility and reusability of the workflow, each individual step of the workflow runs in its own Singularity container. As a consequence, running this workflow has very few individual dependencies. However, it requires Singularity to be installed on the system where the workflow is executed. As the functional installation of Singularity requires root privileges, and Conda currently only provides Singularity for Linux architectures, the installation instructions are slightly different depending on your system/setup:

For most users

If you do not have root privileges on the machine you want to run the workflow on or if you do not have a Linux machine, please install Singularity separately and in privileged mode, depending on your system. You may have to ask an authorized person (e.g., a systems administrator) to do that. This will almost certainly be required if you want to run the workflow on a high-performance computing (HPC) cluster. We have successfully tested the workflow with the following Singularity versions:

• v2.4.5
• v2.6.2
• v3.5.2