Scaling a Variant Calling Genomics Pipeline with FaaS

With the escalating complexity and volume of genomic data, the capacity of biology institutions' HPC faces limitations. While the Cloud presents a viable solution for short-term elasticity, its intricacies pose challenges for bioinformatics users. Alternatively, serverless computing allows for workload scalability with minimal developer burden. However, porting a scientific application to serverless is not a straightforward process. In this article, we present a Variant Calling genomics pipeline migrated from single-node HPC to a serverless architecture. We describe the inherent challenges of this approach and the engineering efforts required to achieve scalability. We contribute by open-sourcing the pipeline for future systems research and as a scalable user-friendly tool for the bioinformatics community.Comment: 6 pages, published at 9th International Workshop on Serverless Computing (WoSC '23), December 11-15, 2023, Bologna, Ital

WTD_EvolApps

Data repository for: Chafin TK, Zbinden ZD, Douglas MR, Martin BT, Middaugh CR, Gray MC, Ballard JR, Douglas ME. 2021. Spatial population genetics in heavily managed species: Separating patterns of historical translocation from contemporary gene flow in white-tailed deer. Evolutionary Applications. In Pres

Aspidoscelis

Repository for Frontiers of Biogeography paper "Taxonomic hypotheses and the biogeography of speciation in the Tiger Whiptail complex (Aspidoscelis tigris: Squamata, Teiidae)

SNT_DDRAD

In progress data repositor

ResistNet_Validation

Data and SnakeMake workflows used to validate ResistNet. Includes simulations + outputs in "simulation/" subdirectory, and an empirical case study in Speckled Dace in "case_study_spd/

autostreamtree_demo

Data from: "autoStreamTree: Genomic variant data fitted to geospatial networks

White River Fish Hybridization

Data repository for: Zbinden, Z. D., Douglas, M. R., Chafin, T. K., & Douglas, M. E. (2023). A community genomics approach to natural hybridization. Proceedings of the Royal Society B, 290(1999), 20230768. https://doi.org/10.1098/rspb.2023.0768

gila_ub_snps.tar

Data files containing an all-SNP alignment (in pyRAD .snps format), unlinked SNPs (=1 sampled per locus) in phylip format, and a filtered unlinked SNP alignment in phylip format. A filtered dataset of unlinked SNPs were used to run STRUCTURE and DAPC. See Methods for more details

gila_ub_introgress.tar.gz

Gzipped tar archive containing input files and R code for running genomic cline analyse