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

ABSTRACT:

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 High-Performance Computing (HPC) environments. Unlike PGGB, nf-core/pangenome distributes align

SUBMITTER: Heumos S 

PROVIDER: S-EPMC11568064 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature