Holistic optimization of an RNA-seq workflow for multi-threaded environments

…, SD Athmalingam Ravishankar… - …, 2019 - academic.oup.com
For many next generation-sequencing pipelines, the most computationally intensive step is
the alignment of reads to a reference sequence. As a result, alignment software such as the …

An investigation on public cloud performance variation for an rna sequencing workflow

D Perez, LH Hung, S Xu, KY Yeung… - Proceedings of the 11th …, 2020 - dl.acm.org
Public Infrastructure-as-a-Service (IaaS) clouds abstract various details regarding the
implementation of resources provided to users. For example, users are not informed about the …

[PDF][PDF] Profiling Resource Utilization of Bioinformatics Workflows

H Deng, LH Hung, R Schooley, D Perez… - arXiv preprint arXiv …, 2020 - researchgate.net
Background We present a software tool, the Container Profiler, that measures and records
the resource usage of any containerized task. Our tool profiles the CPU, memory, disk, and …