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Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data
Analyzing and storing data and results from next-generation sequencing (NGS) experiments is a challenging task, hampered by ever-increasing data volumes and frequent updates of analysis methods and tools. Storage and computation have grown beyond the capacity of personal computers and there is a nee...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3704847/ https://www.ncbi.nlm.nih.gov/pubmed/23800020 http://dx.doi.org/10.1186/2047-217X-2-9 |
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author | Lampa, Samuel Dahlö, Martin Olason, Pall I Hagberg, Jonas Spjuth, Ola |
author_facet | Lampa, Samuel Dahlö, Martin Olason, Pall I Hagberg, Jonas Spjuth, Ola |
author_sort | Lampa, Samuel |
collection | PubMed |
description | Analyzing and storing data and results from next-generation sequencing (NGS) experiments is a challenging task, hampered by ever-increasing data volumes and frequent updates of analysis methods and tools. Storage and computation have grown beyond the capacity of personal computers and there is a need for suitable e-infrastructures for processing. Here we describe UPPNEX, an implementation of such an infrastructure, tailored to the needs of data storage and analysis of NGS data in Sweden serving various labs and multiple instruments from the major sequencing technology platforms. UPPNEX comprises resources for high-performance computing, large-scale and high-availability storage, an extensive bioinformatics software suite, up-to-date reference genomes and annotations, a support function with system and application experts as well as a web portal and support ticket system. UPPNEX applications are numerous and diverse, and include whole genome-, de novo- and exome sequencing, targeted resequencing, SNP discovery, RNASeq, and methylation analysis. There are over 300 projects that utilize UPPNEX and include large undertakings such as the sequencing of the flycatcher and Norwegian spruce. We describe the strategic decisions made when investing in hardware, setting up maintenance and support, allocating resources, and illustrate major challenges such as managing data growth. We conclude with summarizing our experiences and observations with UPPNEX to date, providing insights into the successful and less successful decisions made. |
format | Online Article Text |
id | pubmed-3704847 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-37048472013-07-15 Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data Lampa, Samuel Dahlö, Martin Olason, Pall I Hagberg, Jonas Spjuth, Ola Gigascience Review Analyzing and storing data and results from next-generation sequencing (NGS) experiments is a challenging task, hampered by ever-increasing data volumes and frequent updates of analysis methods and tools. Storage and computation have grown beyond the capacity of personal computers and there is a need for suitable e-infrastructures for processing. Here we describe UPPNEX, an implementation of such an infrastructure, tailored to the needs of data storage and analysis of NGS data in Sweden serving various labs and multiple instruments from the major sequencing technology platforms. UPPNEX comprises resources for high-performance computing, large-scale and high-availability storage, an extensive bioinformatics software suite, up-to-date reference genomes and annotations, a support function with system and application experts as well as a web portal and support ticket system. UPPNEX applications are numerous and diverse, and include whole genome-, de novo- and exome sequencing, targeted resequencing, SNP discovery, RNASeq, and methylation analysis. There are over 300 projects that utilize UPPNEX and include large undertakings such as the sequencing of the flycatcher and Norwegian spruce. We describe the strategic decisions made when investing in hardware, setting up maintenance and support, allocating resources, and illustrate major challenges such as managing data growth. We conclude with summarizing our experiences and observations with UPPNEX to date, providing insights into the successful and less successful decisions made. BioMed Central 2013-06-25 /pmc/articles/PMC3704847/ /pubmed/23800020 http://dx.doi.org/10.1186/2047-217X-2-9 Text en Copyright © 2013 Lampa et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License(http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Review Lampa, Samuel Dahlö, Martin Olason, Pall I Hagberg, Jonas Spjuth, Ola Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data |
title | Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data |
title_full | Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data |
title_fullStr | Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data |
title_full_unstemmed | Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data |
title_short | Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data |
title_sort | lessons learned from implementing a national infrastructure in sweden for storage and analysis of next-generation sequencing data |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3704847/ https://www.ncbi.nlm.nih.gov/pubmed/23800020 http://dx.doi.org/10.1186/2047-217X-2-9 |
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