Nanopore sequencing data analysis using Microsoft Azure cloud computing service
Genetic information provides insights into the exome, genome, epigenetics and structural organisation of the organism. Given the enormous amount of genetic information, scientists are able to perform mammoth tasks to improve the standard of health care such as determining genetic influences on outco...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2022-01-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9718390/?tool=EBI |
| _version_ | 1811178976427638784 |
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| author | Linh Truong Felipe Ayora Lloyd D’Orsogna Patricia Martinez Dianne De Santis |
| author_facet | Linh Truong Felipe Ayora Lloyd D’Orsogna Patricia Martinez Dianne De Santis |
| author_sort | Linh Truong |
| collection | DOAJ |
| description | Genetic information provides insights into the exome, genome, epigenetics and structural organisation of the organism. Given the enormous amount of genetic information, scientists are able to perform mammoth tasks to improve the standard of health care such as determining genetic influences on outcome of allogeneic transplantation. Cloud based computing has increasingly become a key choice for many scientists, engineers and institutions as it offers on-demand network access and users can conveniently rent rather than buy all required computing resources. With the positive advancements of cloud computing and nanopore sequencing data output, we were motivated to develop an automated and scalable analysis pipeline utilizing cloud infrastructure in Microsoft Azure to accelerate HLA genotyping service and improve the efficiency of the workflow at lower cost. In this study, we describe (i) the selection process for suitable virtual machine sizes for computing resources to balance between the best performance versus cost effectiveness; (ii) the building of Docker containers to include all tools in the cloud computational environment; (iii) the comparison of HLA genotype concordance between the in-house manual method and the automated cloud-based pipeline to assess data accuracy. In conclusion, the Microsoft Azure cloud based data analysis pipeline was shown to meet all the key imperatives for performance, cost, usability, simplicity and accuracy. Importantly, the pipeline allows for the on-going maintenance and testing of version changes before implementation. This pipeline is suitable for the data analysis from MinION sequencing platform and could be adopted for other data analysis application processes. |
| first_indexed | 2024-04-11T06:28:06Z |
| format | Article |
| id | doaj.art-31185b59520f403cadf709c4ec2834a8 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-11T06:28:06Z |
| publishDate | 2022-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-31185b59520f403cadf709c4ec2834a82022-12-22T04:40:16ZengPublic Library of Science (PLoS)PLoS ONE1932-62032022-01-011712Nanopore sequencing data analysis using Microsoft Azure cloud computing serviceLinh TruongFelipe AyoraLloyd D’OrsognaPatricia MartinezDianne De SantisGenetic information provides insights into the exome, genome, epigenetics and structural organisation of the organism. Given the enormous amount of genetic information, scientists are able to perform mammoth tasks to improve the standard of health care such as determining genetic influences on outcome of allogeneic transplantation. Cloud based computing has increasingly become a key choice for many scientists, engineers and institutions as it offers on-demand network access and users can conveniently rent rather than buy all required computing resources. With the positive advancements of cloud computing and nanopore sequencing data output, we were motivated to develop an automated and scalable analysis pipeline utilizing cloud infrastructure in Microsoft Azure to accelerate HLA genotyping service and improve the efficiency of the workflow at lower cost. In this study, we describe (i) the selection process for suitable virtual machine sizes for computing resources to balance between the best performance versus cost effectiveness; (ii) the building of Docker containers to include all tools in the cloud computational environment; (iii) the comparison of HLA genotype concordance between the in-house manual method and the automated cloud-based pipeline to assess data accuracy. In conclusion, the Microsoft Azure cloud based data analysis pipeline was shown to meet all the key imperatives for performance, cost, usability, simplicity and accuracy. Importantly, the pipeline allows for the on-going maintenance and testing of version changes before implementation. This pipeline is suitable for the data analysis from MinION sequencing platform and could be adopted for other data analysis application processes.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9718390/?tool=EBI |
| spellingShingle | Linh Truong Felipe Ayora Lloyd D’Orsogna Patricia Martinez Dianne De Santis Nanopore sequencing data analysis using Microsoft Azure cloud computing service PLoS ONE |
| title | Nanopore sequencing data analysis using Microsoft Azure cloud computing service |
| title_full | Nanopore sequencing data analysis using Microsoft Azure cloud computing service |
| title_fullStr | Nanopore sequencing data analysis using Microsoft Azure cloud computing service |
| title_full_unstemmed | Nanopore sequencing data analysis using Microsoft Azure cloud computing service |
| title_short | Nanopore sequencing data analysis using Microsoft Azure cloud computing service |
| title_sort | nanopore sequencing data analysis using microsoft azure cloud computing service |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9718390/?tool=EBI |
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