{"repo":"nf-core/cutandrun","free":true,"listed":false,"github":"https://github.com/nf-core/cutandrun","clone":"git clone https://github.com/nf-core/cutandrun.git","description":"Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.","language":"Nextflow","stars":113,"topics":["nf-core","nextflow","workflow","pipeline","cutandrun-seq","cutandrun","cutandtag-seq","cutandtag"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/cutandrun is a best-practice bioinformatic analysis pipeline for CUT&RUN, CUT&Tag, and TIPseq experimental protocols that were developed to study protein-DNA interactions and epigenomic profiling. CUT&RUN Meers, M. P., Bryson, T. D., Henikoff, J. G., & Henikoff, S. (2019). Improved CUT&RUN chromatin profiling tools. eLife , 8 . https://doi.org/10.7554/eLife.46314 CUT&Tag Kaya-Okur, H. S., Wu, S. J., Codomo, C. A., Pledger, E. S., Bryson, T. D., Henikoff, J. G., Ahmad, K., & Henikoff, S. (2019). CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nature Communications , 10 (1), 1930. https://doi.org/10.1038/s41467-019-09982-5] TIPseq Bartlett, D. A., Dileep, V., Handa, T., Ohkawa, Y., Kimura, H., Henikoff, S., & Gilbert, D. M. (2021). High-throughput single-cell epigenomic profiling by targeted insertion of promoters (TIP-seq). Journal of Cell Biology, 220(12), e202103078. https://doi.org/10.1083/jcb.202103078 The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a portable, reproducible manner. It is capable of using containerisation and package management making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process, which makes it easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules. The pipeline has been ","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/cutandrun/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}