Integrated CRISPR-Cas9 analysis pipeline for targeted and screening genomics

In recent years, CRISPR technology has become widely applied in scientific research, being simpler, cheaper, and more precise than previous gene editing techniques. This editing technology can be used for various applications such as gene knock-out (KO), gene knock-in (KI), CRISPR activation (CRISPRa) and CRISPR interference (CRISPRi), CRISPR screens, base editing (BE) and prime editing (PE). The share of pipelines to capture the variety of CRISPR experimental designs is low and until now none of them caters to both gene editing and CRISPR-based functional genomics. Here we introduce nf-core/crisprseq, a Nextflow DSL2 pipeline for the assessment of CRISPR gene editing and screening assays. The workflow is written in a modularized fashion, to allow the easy incorporation of new steps. nf-core/crisprseq is the first generic pipeline enabling the analysis of the broad spectrum of CRISPR designs. We show its usability by running the pipeline on two example datasets.