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

Simon Heumos1,2,3,4, Michael L Heuer5, Friederike Hanssen1,2,3,4

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Summary
This summary is machine-generated.

nf-core/pangenome is a new pipeline for constructing pangenome graphs. It offers a scalable and efficient reference-unbiased approach, achieving significant speedups compared to existing methods.

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Pangenome graphs capture genomic variability but current methods have biases and scalability issues.
  • Existing tools like PanGenome Graph Builder (PGGB) can exclude complex sequences or rely on references.
  • There is a need for a state-of-the-art pipeline for easy deployment, efficient resource use, and scalability.

Purpose of the Study:

  • To present nf-core/pangenome, a novel pipeline for constructing pangenome graphs.
  • To provide a reference-unbiased, scalable, and efficient solution for pangenome graph construction.
  • To address limitations of existing pangenome graph building methods.

Main Methods:

  • Implemented in Nextflow following nf-core best practices.
  • Utilizes biocontainers for portability and deployment in High-Performance Computing (HPC) environments.
  • Distributes alignments across cluster nodes for enhanced scalability.

Main Results:

  • Successfully constructed pangenome graphs for 1000 human chromosome 19 haplotypes and 2146 Escherichia coli sequences.
  • Achieved a two to threefold speedup compared to PGGB.
  • Demonstrated efficient resource utilization without increasing greenhouse gas emissions.

Conclusions:

  • nf-core/pangenome offers a significant advancement in pangenome graph construction.
  • The pipeline provides a scalable, efficient, and reference-unbiased approach.
  • It is readily deployable and usable in various computational environments.