2020
Huang, P. -J.; Chang, J. -H.; Lin, H. -H.; Li, Y. -X.; Lee, C. -C.; Su, C. -T.; Li, Y. -L.; Chang, M. -T.; Weng, S.; Cheng, W. -H.; Chiu, C. -H.; Tang, P.
DeepVariant-on-Spark: Small-Scale Genome Analysis Using a Cloud-Based Computing Framework Journal Article
In: Computational and Mathematical Methods in Medicine, 2020 , 2020, ISSN: 1748670X, (cited By 1).
Abstract | Links | BibTeX | 標籤: Cloud Computing; Computational Biology; Cost-Benefit Analysis; Deep Learning; Genetic Variation; Genome, Computer; Software; Whole Genome Sequencing, Human; High-Throughput Nucleotide Sequencing; Humans; Neural Networks
@article{Huang2020,
title = {DeepVariant-on-Spark: Small-Scale Genome Analysis Using a Cloud-Based Computing Framework},
author = {P. -J. Huang and J. -H. Chang and H. -H. Lin and Y. -X. Li and C. -C. Lee and C. -T. Su and Y. -L. Li and M. -T. Chang and S. Weng and W. -H. Cheng and C. -H. Chiu and P. Tang},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85091265418&doi=10.1155%2f2020%2f7231205&partnerID=40&md5=d337abe3af557ac2b86d08f201393e81},
doi = {10.1155/2020/7231205},
issn = {1748670X},
year = {2020},
date = {2020-01-01},
journal = {Computational and Mathematical Methods in Medicine},
volume = {2020},
publisher = {Hindawi Limited},
abstract = {Although sequencing a human genome has become affordable, identifying genetic variants from whole-genome sequence data is still a hurdle for researchers without adequate computing equipment or bioinformatics support. GATK is a gold standard method for the identification of genetic variants and has been widely used in genome projects and population genetic studies for many years. This was until the Google Brain team developed a new method, DeepVariant, which utilizes deep neural networks to construct an image classification model to identify genetic variants. However, the superior accuracy of DeepVariant comes at the cost of computational intensity, largely constraining its applications. Accordingly, we present DeepVariant-on-Spark to optimize resource allocation, enable multi-GPU support, and accelerate the processing of the DeepVariant pipeline. To make DeepVariant-on-Spark more accessible to everyone, we have deployed the DeepVariant-on-Spark to the Google Cloud Platform (GCP). Users can deploy DeepVariant-on-Spark on the GCP following our instruction within 20 minutes and start to analyze at least ten whole-genome sequencing datasets using free credits provided by the GCP. DeepVaraint-on-Spark is freely available for small-scale genome analysis using a cloud-based computing framework, which is suitable for pilot testing or preliminary study, while reserving the flexibility and scalability for large-scale sequencing projects. © 2020 Po-Jung Huang et al.},
note = {cited By 1},
keywords = {Cloud Computing; Computational Biology; Cost-Benefit Analysis; Deep Learning; Genetic Variation; Genome, Computer; Software; Whole Genome Sequencing, Human; High-Throughput Nucleotide Sequencing; Humans; Neural Networks},
pubstate = {published},
tppubtype = {article}
}
Although sequencing a human genome has become affordable, identifying genetic variants from whole-genome sequence data is still a hurdle for researchers without adequate computing equipment or bioinformatics support. GATK is a gold standard method for the identification of genetic variants and has been widely used in genome projects and population genetic studies for many years. This was until the Google Brain team developed a new method, DeepVariant, which utilizes deep neural networks to construct an image classification model to identify genetic variants. However, the superior accuracy of DeepVariant comes at the cost of computational intensity, largely constraining its applications. Accordingly, we present DeepVariant-on-Spark to optimize resource allocation, enable multi-GPU support, and accelerate the processing of the DeepVariant pipeline. To make DeepVariant-on-Spark more accessible to everyone, we have deployed the DeepVariant-on-Spark to the Google Cloud Platform (GCP). Users can deploy DeepVariant-on-Spark on the GCP following our instruction within 20 minutes and start to analyze at least ten whole-genome sequencing datasets using free credits provided by the GCP. DeepVaraint-on-Spark is freely available for small-scale genome analysis using a cloud-based computing framework, which is suitable for pilot testing or preliminary study, while reserving the flexibility and scalability for large-scale sequencing projects. © 2020 Po-Jung Huang et al.