nf-core/cutandrun: A Nextflow pipeline for the analysis of CUT&RUN, CUT&Tag and TIP-seq datasets

Awk Python Perl Nextflow Submitted 12 August 2025 • Published 16 March 2026
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Authors

Tamara L. Hodgetts (0000-0002-3991-1683), Charlotte West (0000-0003-2094-3324), Nicholas M. Luscombe (0000-0001-5293-4778), Jernej Ule (0000-0002-2452-4277), James Briscoe (0000-0002-1020-5240), Chris Cheshire (0000-0002-5806-2883)

Citation

Hodgetts et al., (2026). nf-core/cutandrun: A Nextflow pipeline for the analysis of CUT&RUN, CUT&Tag and TIP-seq datasets. Journal of Open Source Software, 11(119), 9672, https://doi.org/10.21105/joss.09672

@article{Hodgetts2026, doi = {10.21105/joss.09672}, url = {https://doi.org/10.21105/joss.09672}, year = {2026}, publisher = {The Open Journal}, volume = {11}, number = {119}, pages = {9672}, author = {Hodgetts, Tamara L. and West, Charlotte and Luscombe, Nicholas M. and Ule, Jernej and Briscoe, James and Cheshire, Chris}, title = {nf-core/cutandrun: A Nextflow pipeline for the analysis of CUT&RUN, CUT&Tag and TIP-seq datasets}, journal = {Journal of Open Source Software} }
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nf-core CUT&RUN CUT&Tag TIP-seq single-cell epigenomics

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