10.25379/uwc.7438616.v1
Peter Van Heusden
Peter
Van Heusden
High Throughput Computing in bioinformatics: workflows, containers and emerging paradigms
University of Western Cape
2018
High Throughput Computing
Bioinformatics
Infrastructure Engineering and Asset Management
Applied Computer Science
2018-12-10 06:40:30
Presentation
https://kikapu.uwc.ac.za/articles/presentation/High_Throughput_Computing_in_bioinformatics_workflows_containers_and_emerging_paradigms/7438616
Next Generation Sequencing has brought genomic analysis within the range
of a great number of laboratories, while increasing the demand for
bioinformatic analysis. These typically comprise workflows composed out
of chains of analyses with data flowing between workflow steps. Such
analysis is amenable to High Throughput Computing, a form of high
performance computing characterised by a focus on overall analysis
throughput rather than optimisation of a single application. In recent
years workflow languages and container technologies have become a key
part in composing efficient, reproducible and re-usable bionformatic
workflows. These technologies, however, pose a challenge for High
Performance Computing providers as they require different
characteristics from an execution environment to that provided by
traditional HPC clusters. These challenges will be discussed and some
approaches to solving them will be discussed.