#8nf-core/cutandrun: A Nextflow pipeline for analysis of CUT&Run, CUT&TAG and TIP-Seq datasets
Chris Cheshire, Charlotte West, and Tamara Hodgetts
We present nf-core/cutandrun, a best-practice bioinformatic analysis workflow for sequencing data generated from the CUT&RUN, CUT&Tag and TIP-Seq protocols. The pipeline supports a rich set of experimental design options including spike-ins, IgG controls, technical replicates and antibody groupings as well as comprehensive quality metric reporting. nf-core/cutandrun is designed to the tenets of portability, reproducibility and interpretability. nf-core/cutandrun runs on a wide range of execution environments, operating systems and platforms and is designed to be used with the minimum of technical knowledge.