PuSH - Publication Server of Helmholtz Zentrum München

Heumos, S.* ; Heuer, M.L.* ; Hanssen, F.* ; Heumos, L. ; Guarracino, A.* ; Heringer, P.* ; Ehmele, P. ; Prins, P.* ; Garrison, E.* ; Nahnsen, S.*

Cluster-efficient pangenome graph construction with nf-core/pangenome.

Bioinformatics 40:btae609 (2024)
Publ. Version/Full Text DOI PMC
Free by publisher
Open Access Green: Postprint online available 11/2025
MOTIVATION: Pangenome 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. RESULTS: To 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 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 E. coli sequences, achieving a two to threefold speedup compared to PGGB without increasing greenhouse gas emissions. AVAILABILITY: 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/1.1.2/docs/usage. SUPPLEMENTARY: Supplementary data are available at Bioinformatics online.
Altmetric
Additional Metrics?
[➜Log in]
Edit extra informations Login
Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
ISSN (print) / ISBN 1367-4803
Journal Bioinformatics
Quellenangaben Volume: 40, Issue: 11, Pages: , Article Number: btae609 Supplement: ,
Publisher Oxford University Press
Publishing Place Oxford
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Institute of Computational Biology (ICB)