Use of application containers and workflows for genomic data analysis

Journal of Pathology Informatics
Wade L SchulzRichard Torres

Abstract

The rapid acquisition of biological data and development of computationally intensive analyses has led to a need for novel approaches to software deployment. In particular, the complexity of common analytic tools for genomics makes them difficult to deploy and decreases the reproducibility of computational experiments. Recent technologies that allow for application virtualization, such as Docker, allow developers and bioinformaticians to isolate these applications and deploy secure, scalable platforms that have the potential to dramatically increase the efficiency of big data processing. While limitations exist, this study demonstrates a successful implementation of a pipeline with several discrete software applications for the analysis of next-generation sequencing (NGS) data. With this approach, we significantly reduced the amount of time needed to perform clonal analysis from NGS data in acute myeloid leukemia.

References

Jan 14, 2010·Current Protocols in Molecular Biology·Daniel BlankenbergJames Taylor
Nov 9, 2010·Nature Biotechnology·Joel T Dudley, Atul J Butte
Aug 18, 2012·Nature Reviews. Genetics·Anton Nekrutenko, James Taylor
May 3, 2013·The New England Journal of Medicine·UNKNOWN Cancer Genome Atlas Research NetworkGreg Eley
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Aug 16, 2016·The New England Journal of Medicine·Harlan M Krumholz, Joanne Waldstreicher

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Citations

Aug 8, 2018·GigaScience·Pai ZhangKa Yee Yeung
Feb 5, 2019·Journal of Ultrasound in Medicine : Official Journal of the American Institute of Ultrasound in Medicine·Adrian D HaimovichR Andrew Taylor
Aug 14, 2018·Bioinformatics·Jon Ander NovellaOla Spjuth
Nov 29, 2017·F1000Research·Aleksandr AgafonovLars Ailo Bongo
Nov 2, 2017·Journal of the American Medical Informatics Association : JAMIA·Reem AlmugbelKa Yee Yeung
Jun 2, 2020·Journal of Pathology Informatics·Thomas J S DurantWade L Schulz
Jan 8, 2019·BMC Bioinformatics·Indresh SinghKaren E Nelson
Aug 20, 2019·Expert Review of Molecular Diagnostics·Yin Kwan Evelyn WongSze Chuen Cesar Wong

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Methods Mentioned

BETA
exome sequencing

Software Mentioned

Linux
CentOS7
Python
Kubernetes
Docker
Luigi
Docker containers
sysbench
SciClone
CentOS

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