ReviewGenome biology2025
Empowering bioinformatics communities with Nextflow and nf-core.
Abstract readReview
In one paragraph
Review in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
0numbers the graph read from it
0cells of the map it votes in
38citing papers in PubMed
–field-weighted citation impact
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
38 citing papers in PubMed.
- Developmental contexts of gene-regulatory evolution following whole genome duplication in salmonids.Nature ecology & evolution · 2026Article
- Modeling lung adenocarcinoma using layer-by-layer nanoparticles mitigates innate immune cell activation.bioRxiv : the preprint server for biology · 2026Article
- A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq nanopore long reads data.NAR genomics and bioinformatics · 2026Article
- Community-driven updates for comprehensive long-read metagenomics and enhanced binning in nf-core/mag v5.Bioinformatics (Oxford, England) · 2026Article
- Supporting workflow reproducibility by linking bioinformatics tools across papers and executable code.Bioinformatics (Oxford, England) · 2026Article
- Mapping the path to clinical implementation of multi-omics.Nature genetics · 2026Review
- The Single-Cell Pediatric Cancer Atlas: Data portal and open-source tools for single-cell transcriptomics of pediatric tumors.Cell genomics · 2026Article
- nf-core/magmap: Map metatranscriptomes to large collections of genomes.Bioinformatics (Oxford, England) · 2026Article
- Ten quick tips to SNIFF out sustainable and secure scientific software.PLoS computational biology · 2026Article
- LAFA: A Framework for Reproducible Longitudinal Assessment of Protein Function Annotation Models.ArXiv · 2026Article
- OrthoGuide: A Database for Rooting Inference of Orthologous Genes.Genome biology and evolution · 2026Article
- systemPipeR: a multipurpose workflow management system for reproducible data analysis.NAR genomics and bioinformatics · 2026Article
- Beyond Data: Artificial intelligence, knowledge graphs, and the next revolution in wheat breeding.Plant communications · 2026Review
- Intratumoral Microbiome of Metastatic Pancreatic Ductal Adenocarcinoma.International journal of molecular sciences · 2026Article
- nf-core/viralmetagenome: A novel pipeline for untargeted viral genome reconstruction.Bioinformatics (Oxford, England) · 2026Article
- Article
- TaxTriage: an open-source metagenomic sequencing data analysis pipeline enabling putative pathogen detection.Bioinformatics (Oxford, England) · 2026Article
- Nallo: a Nextflow pipeline for comprehensive human long-read genome analysis.Bioinformatics (Oxford, England) · 2026Article
- Expression Atlas in 2026: enabling FAIR and open expression data through community collaboration and integration.Nucleic acids research · 2026Article
- GxP-Ready Single-Cell RNA-seq and Spatial Transcriptomics End-to-End Pipeline for Clinical Research.Computational and structural biotechnology journal · 2026Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
44 authors.
Björn E LangerCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.
Andreia AmaralMED. University of Évora, Polo da Mitra, Évora, 7002-554, Portugal.
Marie-Odile BaudementCentre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, Ås, 1430, Norway.
Franziska BonathKungliga Techniska Högskolan, School of Engineering Sciences in Chemistry, Biotechnology and Health at the Department of Gene Technology, Stockholm, Sweden.
Mathieu CharlesINRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, F-78350, France.
Praveen Krishna ChitneediResearch Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, Dummerstorf, 18196, Germany.
Emily L ClarkThe Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin, UK.
Paolo Di TommasoSeqera, Carrer de Marià Aguiló, 28, Barcelona, 08005, Spain.
Sarah DjebaliIRSD, Université de Toulouse, INSERM, INRAE, ENVT, Univ Toulouse III - Paul Sabatier (UPS), Toulouse, France.
Philip A EwelsSeqera, Carrer de Marià Aguiló, 28, Barcelona, 08005, Spain.
Sonia EynardGenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, 31326, France.
James A Fellows YatesDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany.
Daniel FischerNatural Resources Institute Finland (Luke), Applied Statistical Methods, Myllytie 1, Jokioinen, 31600, Finland.
Evan W FlodenSeqera, Carrer de Marià Aguiló, 28, Barcelona, 08005, Spain.
Sylvain FoissacGenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, 31326, France.
Gisela GabernetDepartment of Pathology, Yale School of Medicine, New Haven, CT, 06511, USA.
Maxime U GarciaSeqera, Carrer de Marià Aguiló, 28, Barcelona, 08005, Spain.
Gareth GillardCentre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, Ås, 1430, Norway.
Manu Kumar GundappaThe Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin, UK.
Cervin GuyomarGenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, 31326, France.
Christopher HakkaartSeqera, Carrer de Marià Aguiló, 28, Barcelona, 08005, Spain.
Friederike HanssenBiomedical Data Science, Department of Computer Science, University of Tübingen, Tübingen, Germany.
Peter W HarrisonEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
Matthias HörtenhuberDepartment of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
Cyril KuryloGenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, 31326, France.
Christa KühnResearch Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, Dummerstorf, 18196, Germany.
Sandrine LagarriguePEGASE, INRAE, Institut Agro, Saint Gilles, 35590, France.
Delphine LalliasINRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, F-78350, France.
Daniel J MacqueenThe Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin, UK.
Edmund MillerDepartment of Biological Sciences and Center for Systems Biology, The University of Texas at Dallas, Richardson, TX, 75205, USA.
Júlia Mir-PedrolQuantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany.
Gabriel Costa Monteiro MoreiraUnit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
Sven NahnsenBiomedical Data Science, Department of Computer Science, University of Tübingen, Tübingen, Germany.
Harshil PatelSeqera, Carrer de Marià Aguiló, 28, Barcelona, 08005, Spain.
Alexander PeltzerBoehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Straße 65, Biberach/Riss, 88400, Germany.
Frederique PitelGenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, 31326, France.
Yuliaxis Ramayo-CaldasAnimal Breeding and Genetics Program, Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, Barcelona, Spain.
Marcel da Câmara Ribeiro-DantasSeqera, Carrer de Marià Aguiló, 28, Barcelona, 08005, Spain.
Dominique RochaINRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, F-78350, France.
Mazdak SalavatiThe Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin, UK.
Alexey SokolovEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
Jose Espinosa-CarrascoCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain. joseantonio.espinosa@crg.eu.
Cedric NotredameCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain. cedric.notredame@crg.eu.
The Nf-Core Community
Funding
Carl-Zeiss-Stiftung Certification and Foundations of Safe Machine Learning Systems in HealthcareDeutsche Forschungsgemeinschaft EXC 2180 - 390900677 (iFIT)Horizon 2020 research and innovation programme, European Union 101000213 (HoloRuminant)Horizon 2020 research and innovation programme, European Union 101000236 (GEroNIMO)Horizon 2020 research and innovation programme, European Union 815668 (BovReg)Horizon 2020 research and innovation programme, European Union 817923 (AQUA-FAANG)Horizon 2020 research and innovation programme, European Union 817998 (GENE-SWitCH)Horizon Europe programme, European Union 101094718 (EuroFAANG Research Infrastructure)Werner Siemens-Stiftung Palaeobiotechnology
Abstract
Standardized analysis pipelines contribute to making data bioinformatics research compliant with the paradigm of Findability, Accessibility, Interoperability, and Reusability (FAIR), and facilitate collaboration. Nextflow and Snakemake, two popular command-line solutions, are increasingly adopted by users, complementing GUI-based platforms such as Galaxy. We report recent developments of the nf-core framework with the new Nextflow Domain-Specific Language (DSL2). An extensive library of modules and subworkflows enables research communities to adopt common standards progressively, as resources and needs allow. We present an overview of some of the research communities built around nf-core and showcase its adoption by six EuroFAANG farmed animal research consortia.
Indexed as
Computational BiologySoftwareAnimals
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What OpenQuestion holds
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LicenceCC BY-NC-ND
Read underepoch 390
Registered trials
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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.