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arXiv · 2505.02195

Scalable Genomic Context Analysis with GCsnap2 on HPC Clusters

Reto Krummenacher·Osman Seckin Simsek·Michèle Leemann·Leila T. Alexander·Torsten Schwede·Florina M. Ciorba·Joana Pereira
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Abstract

GCsnap2 Cluster is a scalable, high performance tool for genomic context analysis, developed to overcome the limitations of its predecessor, GCsnap1 Desktop. Leveraging distributed computing with mpi4py[.]futures, GCsnap2 Cluster achieved a 22x improvement in execution time and can now perform genomic context analysis for hundreds of thousands of input sequences in HPC clusters. Its modular architecture enables the creation of task-specific workflows and flexible deployment in various computational environments, making it well suited for bioinformatics studies of large-scale datasets. This work highlights the potential for applying similar approaches to solve scalability challenges in other scientific domains that rely on large-scale data analysis pipelines.

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Reto Krummenacher, Osman Seckin Simsek, Michèle Leemann, Leila T. Alexander, Torsten Schwede, Florina M. Ciorba, Joana Pereira. 2025-05-04. Scalable Genomic Context Analysis with GCsnap2 on HPC Clusters. https://doi.org/10.1145/3732775.3733579

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