# nf-core/crisprseq: a versatile pipeline for comprehensive analysis of CRISPR gene editing and screening assays

## TL;DR

This paper introduces a new pipeline for analyzing CRISPR gene editing and screening, offering a versatile and modular solution for various CRISPR applications.

## Contribution

The paper presents the first generic pipeline for comprehensive CRISPR analysis, supporting both gene editing and functional genomics.

## Key findings

- nf-core/crisprseq is modular and allows easy incorporation of new analysis steps.
- The pipeline is demonstrated to be effective using publicly available datasets.
- It supports a wide range of CRISPR applications, including gene knockout and base editing.

## Abstract

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 knockout, gene knock-in, CRISPR activation (CRISPRa), CRISPR interference (CRISPRi), CRISPR screens, base editing, and prime editing. The share of pipelines to analyze the variety of CRISPR editing methods 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 the performance and usability of the software using publicly available datasets.