The International Conference for High Performance Computing, Networking, Storage, and Analysis
The International Conference for High Performance Computing, Networking, Storage, and Analysis
Poster Type: ACM Student Research Competition, Undergraduate
Author: Naomi Kolodisner (University of Arizona), Alok Kamatar (Advisor) (University of Chicago), J. Greg Pauloski (Advisor) (NVIDIA Corporation)
Supervisor: Kyle Chard (University of Chicago)
Abstract: Fecal microbial transplant (FMT) is an effective procedure for restoring gut microbiome balance in patients with Clostridioides difficile infection by introducing healthy donor microbes. Tracking viral genomes during FMT provides insight into microbial community transfer and recovery. We developed a viral detection workflow that processes metagenomic samples to identify, dereplicate, cluster, and annotate viral sequences using GeNomad, CheckV, MMseqs2, and BLAST. The workflow links viral sequences to donor and patient samples, enabling longitudinal tracking. Traditionally, such workflows run sequentially with predefined tools and steps. We compare this workflow against an agent-based workflow that selects the viral detection tool dynamically based on the sequence quality and database match scores of prior samples. Scaling experiments show that parallelizing the workflow using Parsl reduces runtime by over 50%. Tool comparison demonstrates trade-offs in speed, quality, and match ratio, demonstrating the benefits of adaptive, agent-driven workflows for scalable viral detection in microbiome studies.
Best Poster Finalist (BP): no
Poster: PDF
Poster Summary: PDF