ArticleBioinformatics (Oxford, England)2024
Cluster-efficient pangenome graph construction with nf-core/pangenome.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Haplotype graph analysis of PdR1 uncovers resistance diversity to Pierce's disease in Vitis arizonica and its hybrids.G3 (Bethesda, Md.) · 2026Article
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- Approaches to Studying Viral Pangenome Variation Graphs.Genomics, proteomics & bioinformatics · 2026Review
- Accessing medically relevant complex regions with a pangenome graph of 20 near-complete Japanese haplotypes.Nature communications · 2026Article
- Dynamics of genome evolution in the era of pangenome analysis.Cell genomics · 2026Review
- Intraspecies sequence-graph analysis of the Phytophthora theobromicola genome reveals a dynamic structure and variable effector repertoires.G3 (Bethesda, Md.) · 2026Article
- Panalyze: automated virus pangenome variation graph construction, analysis and annotation.Bioinformatics advances · 2026Article
- Puzzler: scalable one-command platinum-quality genome assembly from HiFi and Hi-C.Bioinformatics advances · 2026Article
- Holistic genome assembly and analysis of theIMA fungus · 2026Article
- Dissection of the Ren6 and Ren7 powdery mildew resistance loci in Vitis piasezkii DVIT2027 using phased parental-progeny genomes and intraspecific locus graph reconstruction.G3 (Bethesda, Md.) · 2025Article
- Current State of Fish Reference Genome and Pangenome: Methodologies, Sampling Strategies, Quality Assessment and Future Perspectives to Aquaculture Breeding.Marine biotechnology (New York, N.Y.) · 2025Review
- MetaflowX: a scalable and resource-efficient workflow for multi-strategy metagenomic analysis.Nucleic acids research · 2025Article
- Article
- Review
- Pangenome graphs and their applications in biodiversity genomics.Nature genetics · 2025Review
- Early Detection of BothInternational journal of molecular sciences · 2024Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
motivationPangenome graphs offer a comprehensive way of capturing genomic variability across multiple genomes. However, current construction methods often introduce biases, excluding complex sequences or relying on references. The PanGenome Graph Builder (PGGB) addresses these issues. To date, though, there is no state-of-the-art pipeline allowing for easy deployment, efficient and dynamic use of available resources, and scalable usage at the same time.
resultsTo overcome these limitations, we present nf-core/pangenome, a reference-unbiased approach implemented in Nextflow following nf-core's best practices. Leveraging biocontainers ensures portability and seamless deployment in High-Performance Computing (HPC) environments. Unlike PGGB, nf-core/pangenome distributes alignments across cluster nodes, enabling scalability. Demonstrating its efficiency, we constructed pangenome graphs for 1000 human chromosome 19 haplotypes and 2146 Escherichia coli sequences, achieving a two to threefold speedup compared to PGGB without increasing greenhouse gas emissions. AVAILABILITY AND IMPLEMENTATION: nf-core/pangenome is released under the MIT open-source license, available on GitHub and Zenodo, with documentation accessible at https://nf-co.re/pangenome/docs/usage.
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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.