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Related Experiment Video

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Author Spotlight: Advancing Pathogen Detection and Disease Assessment in Real-Time Using M-ROSE
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SRA Down Under: Cache and Analysis Platform for Infectious Disease.

Thom Cuddihy1, Brian Forde2, Nicholas Rhodes3

  • 1QFAB Bioinformatics - Research Computing Centre, University of Queensland, Australia.

Studies in Health Technology and Informatics
|August 10, 2019
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Summary
This summary is machine-generated.

A local Australian Sequence Read Archive (SRA) cache was established to speed up genomic data analysis, crucial for timely responses during bacterial outbreaks. This pilot project successfully cached seventeen bacterial species, enabling faster research and clinical investigations.

Keywords:
CromwellMeDiCIQRIScloudQueensland GenomicsSRA

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Area of Science:

  • Bioinformatics
  • Genomics
  • Data Science

Background:

  • The Sequence Read Archive (SRA) at the National Center for Biotechnology Information (NCBI) is a critical global repository for sequenced reads.
  • Geographical distance to offshore SRA servers can cause significant delays in accessing data, impacting time-sensitive research and clinical applications, especially during disease outbreaks.

Purpose of the Study:

  • To establish a local Australian SRA cache to mitigate data access delays.
  • To implement a functional data caching system for genomic reads within Australia.
  • To enable local analysis of cached data for research and clinical purposes.

Main Methods:

  • Leveraged NeCTAR Research Cloud, QRIScloud's High-Throughput Computing (HTC) infrastructure, and MeDiCI data fabric for hosting and storage.
  • Employed Cromwell for workflow management and a PostgreSQL database for metadata.
  • Developed a Python Flask application for coordination.
  • Cached data for seventeen bacterial species.

Main Results:

  • Successfully established a local Australian SRA cache.
  • Demonstrated the capability to perform local data analysis, including quality control and taxonomic profiling.
  • Enabled both individual and multiple sample analyses using cached data.

Conclusions:

  • The local SRA cache pilot successfully addressed data access delays for Australian researchers.
  • The system demonstrated utility for time-critical genomic analysis, such as during bacterial outbreaks.
  • Future expansion requires addressing storage needs due to the exponential growth of sequencing data in the SRA.