Nf-LO: A Scalable, Containerized Workflow for Genome-to-Genome Lift Over. (12th August 2021)

• Record Type: Journal Article
• Authors: Talenti, Andrea; Prendergast, James
• Editors: Fraser, Bonnie
• Is Part Of: Genome biology and evolution. Volume 13:Number 9(2021)
• Publication Date: 2021-08-12
• Subjects: liftover -- assembly -- Nextflow -- workflow; Genomics -- Periodicals; Genes -- Periodicals; 572.8605
• DOI: 10.1093/gbe/evab183
• Languages: English
• ISSNs: 1759-6653

Abstract

Abstract: The increasing availability of new genome assemblies often comes with a paucity of associated genomic annotations, limiting the range of studies that can be performed. A common workaround is to lift over annotations from better annotated genomes. However, generating the files required to perform a lift over is computationally and labor intensive and only a limited number are currently publicly available. Here we present nf-LO (nextflow-LiftOver), a containerized and scalable Nextflow pipeline that enables lift overs within and between any species for which assemblies are available. nf-LO will consequently facilitate data interpretation across a broad range of genomic studies.