Scalable in-memory processing of omics workflows.

ABSTRACT: We present a proof of concept implementation of the in-memory computing paradigm that we use to facilitate the analysis of metagenomic sequencing reads. In doing so we compare the performance of POSIX™file systems and key-value storage for omics data, and we show the potential for integrating high-performance computing (HPC) and cloud native technologies. We show that in-memory key-value storage offers possibilities for improved handling of omics data through more flexible and faster data processing. We envision fully containerized workflows and their deployment in portable micro-pipelines with multiple instances working concurrently with the same distributed in-memory storage. To highlight the potential usage of this technology for event driven and real-time data processing, we use a biol

SUBMITTER: Elisseev V 

PROVIDER: S-EPMC9052061 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature