SRA Down Under: Cache and Analysis Platform for Infectious Disease.
Stud Health Technol Inform
; 266: 76-82, 2019 Aug 08.
Article
em En
| MEDLINE
| ID: mdl-31397305
ABSTRACT
SRA, NCBI's Sequence Read Archive, is a valuable resource holding a near definitive collection of the world's collective sequenced reads for academic purposes. Increasingly, these reads are being used for both basic research and clinical investigations. When time is a critical factor in analysis, such as during bacterial outbreaks, the geographical separation between Australia and the offshore NCBI SRA servers can result in significant delays that may have adverse clinical outcomes. To address this, Queensland Genomics commissioned a pilot program for the establishment of a local Australian SRA Cache. Utilizing the hosting capabilities of the NeCTAR Research Cloud, QRIScloud's HTC infrastructure and the MeDiCI data fabric as a storage solution, and the software stack of Cromwell for workflow management, PostgreSQL database for sample and job metadata, and a coordinator Python Flask application, a local cache of seventeen bacterial species was established. Furthermore, the workflow capabilities of Cromwell were leveraged to provide analysis solutions for cached sample data, including quality control and taxonomic profiling, and individual and multiple sample analysis. Moving forward to a broader rollout of increased bacterial species, it was found that the initial storage estimation did not keep up with the exponential increase sequencing reads uploaded to NCBI SRA, which while highlighting the increasing availability and importance in modern research, will need to be addressed.
Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Software
/
Bases de Dados Genéticas
País/Região como assunto:
Oceania
Idioma:
En
Revista:
Stud Health Technol Inform
Assunto da revista:
INFORMATICA MEDICA
/
PESQUISA EM SERVICOS DE SAUDE
Ano de publicação:
2019
Tipo de documento:
Article
País de afiliação:
Austrália