{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Mir-Pedrol J"],"funding":["Higher Education Authority of Ireland","University of Tübingen","CMFI","AICRIstart","Deutsche Forschungsgemeinschaft","Carl Zeiss Foundation"],"pagination":["lqaf214"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12805889"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["8(1)"],"pubmed_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"],"journal":["NAR genomics and bioinformatics"],"pubmed_title":["nf-core/crisprseq: a versatile pipeline for comprehensive analysis of CRISPR gene editing and screening assays."],"pmcid":["PMC12805889"],"funding_grant_id":["20/FFP-P/8641","EXC 2124-390 838 134","EXC 2180—390 900 677"],"pubmed_authors":["Ryan CJ","Gabernet G","Sanvicente-Garcia M","Yazar M","Nf-Core Community","Bonfanti M","Guell M","Kuhlburger L","Mir-Pedrol J","Nahnsen S","Krakau S"],"additional_accession":[]},"is_claimable":false,"name":"nf-core/crisprseq: a versatile pipeline for comprehensive analysis of CRISPR gene editing and screening assays.","description":"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","dates":{"release":"2026-01-01T00:00:00Z","publication":"2026 Mar","modification":"2026-06-10T05:23:21.809Z","creation":"2026-06-10T03:07:22.101Z"},"accession":"S-EPMC12805889","cross_references":{"pubmed":["41551929"],"doi":["10.1093/nargab/lqaf214"]}}