ArticleGenome biology and evolution2021
nf-LO: A Scalable, Containerized Workflow for Genome-to-Genome Lift Over.
Article in Genome biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
15 citing papers in PubMed.
- Article
- Gene regulatory innovations from transposable elements in primate cerebellum development.Nature communications · 2026Article
- Minimizing reference bias with an imputed personalized reference.Genome research · 2026Article
- The complete genome of the KOLF2.1J reference iPSC line.bioRxiv : the preprint server for biology · 2026Article
- The evolution of gene regulation in mammalian cerebellum development.Science (New York, N.Y.) · 2026Article
- Pangenome graph mitigates heterozygosity overestimation from mapping bias: a case study in Chinese indigenous pigs.BMC biology · 2025Article
- Prediction of transcript isoforms and identification of tissue-specific genes in cucumber.BMC genomics · 2025Article
- A comprehensive water buffalo pangenome reveals extensive structural variation linked to population-specific signatures of selection.GigaScience · 2025Article
- Temporal genomics in Hawaiian crickets reveals compensatory intragenomic coadaptation during adaptive evolution.Nature communications · 2024Article
- BCFtools/liftover: an accurate and comprehensive tool to convert genetic variants across genome assemblies.Bioinformatics (Oxford, England) · 2024Article
- Improved sequence mapping using a complete reference genome and lift-over.Nature methods · 2024Article
- The complete sequence of a human Y chromosome.Nature · 2023Article
- Article
- polishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies.Genome biology and evolution · 2023Article
- The conservation of human functional variants and their effects across livestock species.Communications biology · 2022Article
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Authors and funding
2 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.