Work

Enabling microbiome research on personal devices

Year: 2021

Type: conference-paper

Abstract: Microbiome studies have recently transitioned from experimental designs with a few hundred samples to designs spanning tens of thousands of samples. Modern studies such as the Earth Microbiome Project (EMP) afford the statistics crucial for untangling the many factors that influence microbial community composition. Analyzing those data used to require access to a compute cluster, making it both expensive and inconvenient. We show that recent improvements in both hardware and software now allow to compute key bioinformatics tasks on EMP-sized data in minutes using a gaming-class laptop, enabling much faster and broader microbiome science insights.

Source: IEEE International Conference on eScience

DOI: 10.1109/escience51609.2021.00035

Authors: Igor Sfiligoi, Daniel McDonald, Rob Knight

Institutions: San Diego Supercomputer Center, University of California San Diego

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: National Science Foundation, National Research Foundation

Awards: CI-New: Cognitive Hardware and Software Ecosystem Community Infrastructure (CHASE-CI), CC* NPEO: Toward the National Research Platform, CC*DNI DIBBs: The Pacific Research Platform, RAPID: Improving QIIME 2 and UniFrac for Viruses to Respond to COVID-19