You have some RNA-Seq samples and want to know what’s in them? You urgently need to get these RNA-Seq results but your resident bioinformatician is on vacation — again? You have an extensive SRA query with hundreds of libraries to analyze and you don’t know where to start? If any of those questions sound familiar, check out ZARP!

Developed by researchers at the University of Basel, ZARP is a generic RNA-Seq analysis pipeline that allows you to analyze your Illumina short-read sequencing libraries without a lot of bioinformatics experience. ZARP preprocesses (Cutadapt), aligns (STAR), quantifies (kallisto, Salmon) and annotates (ALFA) your sequencing reads, runs quality control (FASTQC, TIN scores) and a principal component analysis on your samples, and produces a report with (mostly) interactive visualizations (MultiQC). ZARP is written in Snakemake, is reasonably fast and not very resource-hungry.

To make it easy to ZARP your samples, the researchers provide ZARP-cli, a convenient command-line interface for starting ZARP runs. ZARP-cli downloads libraries straight from SRA and manages genome resources as well as your default settings, allowing you to trigger ZARP very quickly after initial setup. ZARP-cli also infers missing metadata required for the analysis (read orientation, adapter sequences or even the source organism) from the data itself, which is very useful for meta-analyses or those cases where the person who prepared the original library is now the CEO of a unicorn (good for them!) and doesn’t respond to your insignificant emails and all their notebooks burned to ashes in that fire last year.