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Genomics in the Cloud
Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
2021 (English)Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
Abstract [en]

The continued cost reduction for sequencing genomics data is causing an exponentialgrowth in the amount of data available. Moving both storage and calculation of thisdata to the cloud has been a common trend, but the way to do it is not alwaysobvious. This report compares three different alternatives for doing ad-hoc queries ina cloud based setting: two solutions using data lakes and one solution using arelational database hosted in the cloud. The data lake solutions proved to be easy toset up and fully functional for querying genomics data. The relational database wasmore complicated to set up, but the queries were more time efficient and more costefficient when performing more than 1200 queries per month on at least 100GB ofdata. To make the cloud computing possible for genomics data it had to betransformed into a file format supported by the cloud providers. For this purpose theParquet file format was chosen, tested, and proven to work well

Place, publisher, year, edition, pages
2021. , p. 52
Series
UPTEC IT, ISSN 1401-5749 ; 21030
Keywords [en]
Cloud, IT, Genomics, GCP, AWS
National Category
Other Computer and Information Science
Identifiers
URN: urn:nbn:se:uu:diva-453802OAI: oai:DiVA.org:uu-453802DiVA, id: diva2:1596566
External cooperation
Data Ductus
Educational program
Master of Science Programme in Information Technology Engineering
Supervisors
Examiners
Available from: 2021-09-23 Created: 2021-09-22 Last updated: 2021-09-23Bibliographically approved

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CiteExportLink to record
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Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
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