nf-core/cutandrun: A Nextflow pipeline for the analysis of CUT&RUN, CUT&Tag and TIP-seq datasets
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Tamara Hodgetts Charlotte West Nicholas Luscombe Jernej Ule James Briscoe Chris CheshireAbstract
Mapping transcription factor binding events and histone modifications on a genome-wide scale is key to understanding the regulatory dynamics controlling gene expression. CUT&RUN, CUT&Tag and TIP-seq protocols provide new avenues to map chromatin-associated proteins, offering advantages compared to ChIP-seq in terms of sensitivity, resolution and sample consumption. Despite differences in biochemistry, the core computational analysis of CUT&RUN, CUT&Tag and TIP-seq data exhibit notable similarities, representing an opportunity for a unified bioinformatics solution.
Here, we present nf-core/cutandrun, a best-practice bioinformatics pipeline for CUT&RUN, CUT&Tag and TIP-seq data. In contrast to existing alternative pipelines, nf-core/cutandrun was developed based on the nf-core community framework to provide enhanced reproducibility,
flexibility, scalability, portability and robustness. nf-core/cutandrun additionally enables the specification of spike-in genomes with different normalisation options, supports multiple peak callers, and provides extensive quality control metrics reporting. The pipeline supports a wide range of execution environments and operating systems, and is usable with minimal technical knowledge. We encourage user engagement with the wider nf-core community through the official nf-core GitHub repository and Slack channels, and aim to incorporate feedback in
subsequent releases to ensure that the pipeline remains dynamic and up-to-date.
Journal details
Journal
Journal of Open Source Software
Volume
11
Issue number
119
Pages
9672
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