Rapid GPU-Based Pangenome Graph Layout

Computational Pangenomics is an emerging field that studies genetic variation using a graph structure encompassing multiple genomes. Visualizing pangenome graphs is vital for understanding genome diversity. Yet, handling large graphs can be challenging due to the high computational demands of the gr...

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Vydáno v:SC24: International Conference for High Performance Computing, Networking, Storage and Analysis s. 1 - 19
Hlavní autoři: Li, Jiajie, Schmelzle, Jan-Niklas, Du, Yixiao, Heumos, Simon, Guarracino, Andrea, Guidi, Giulia, Prins, Pjotr, Garrison, Erik, Zhang, Zhiru
Médium: Konferenční příspěvek
Jazyk:angličtina
Vydáno: IEEE 17.11.2024
Témata:
Bioinformatics
Genomics
GPU acceleration
Graph layout
High performance computing
Layout
Measurement
Merging
Pangenomics
Parallel processing
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Shrnutí:Computational Pangenomics is an emerging field that studies genetic variation using a graph structure encompassing multiple genomes. Visualizing pangenome graphs is vital for understanding genome diversity. Yet, handling large graphs can be challenging due to the high computational demands of the graph layout process. In this work, we conduct a thorough performance characterization of a state-of-the-art pangenome graph layout algorithm, revealing significant data-level parallelism, which makes GPUs a promising option for compute acceleration. However, irregular data access and the algorithm's memory-bound nature present significant hurdles. To overcome these challenges, we develop a solution implementing three key optimizations: a cache-friendly data layout, coalesced random states, and warp merging. Additionally, we propose a quantitative metric for scalable evaluation of pangenome layout quality. Evaluated on 24 human whole-chromosome pangenomes, our GPU-based solution achieves a 57.3x speedup over the state-of-the-art multithreaded CPU baseline without layout quality loss, reducing execution time from hours to minutes.
DOI:10.1109/SC41406.2024.00035